Multiple sequence alignment - TraesCS2D01G221100

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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 TraesCS2D01G221100 chr2D 100.000 2459 0 0 1 2459 188554120 188551662 0.000000e+00 4542.0
1 TraesCS2D01G221100 chr2D 94.719 303 15 1 1 302 188586496 188586194 1.030000e-128 470.0
2 TraesCS2D01G221100 chr2D 93.750 304 18 1 1 303 137252795 137253098 2.880000e-124 455.0
3 TraesCS2D01G221100 chr2B 94.373 2168 103 11 304 2459 244871640 244869480 0.000000e+00 3310.0
4 TraesCS2D01G221100 chr2B 84.375 64 5 1 714 777 668053361 668053419 9.500000e-05 58.4
5 TraesCS2D01G221100 chr2A 93.154 2191 107 11 303 2459 202107238 202105057 0.000000e+00 3175.0
6 TraesCS2D01G221100 chr2A 95.420 1441 56 9 303 1738 202840212 202838777 0.000000e+00 2287.0
7 TraesCS2D01G221100 chr2A 77.592 299 57 10 405 700 714497790 714497499 3.250000e-39 172.0
8 TraesCS2D01G221100 chr7A 85.115 786 100 14 1685 2459 584396464 584395685 0.000000e+00 787.0
9 TraesCS2D01G221100 chr7A 85.020 761 103 8 1709 2459 667942613 667941854 0.000000e+00 763.0
10 TraesCS2D01G221100 chr7A 74.247 299 61 13 406 700 303858003 303857717 7.190000e-21 111.0
11 TraesCS2D01G221100 chr6D 84.447 778 113 6 1688 2457 13033352 13032575 0.000000e+00 760.0
12 TraesCS2D01G221100 chr6D 94.737 304 15 1 1 303 401205282 401204979 2.860000e-129 472.0
13 TraesCS2D01G221100 chr6D 94.719 303 15 1 1 302 401259942 401259640 1.030000e-128 470.0
14 TraesCS2D01G221100 chr7D 84.399 782 111 7 1687 2459 538241640 538240861 0.000000e+00 758.0
15 TraesCS2D01G221100 chr7D 84.306 771 108 10 1685 2446 625029204 625028438 0.000000e+00 741.0
16 TraesCS2D01G221100 chr5D 84.685 777 100 16 1699 2459 546676852 546677625 0.000000e+00 758.0
17 TraesCS2D01G221100 chr5D 94.389 303 16 1 1 302 285989894 285990196 4.790000e-127 464.0
18 TraesCS2D01G221100 chr5D 94.079 304 16 2 1 303 286159775 286160077 6.200000e-126 460.0
19 TraesCS2D01G221100 chr3B 84.000 700 97 10 1749 2435 228692185 228692882 0.000000e+00 658.0
20 TraesCS2D01G221100 chr4A 81.586 782 128 12 1686 2457 437496041 437496816 1.240000e-177 632.0
21 TraesCS2D01G221100 chr4A 76.868 281 54 9 405 682 392046189 392045917 5.480000e-32 148.0
22 TraesCS2D01G221100 chr1D 82.507 766 91 18 1690 2444 391245138 391244405 1.240000e-177 632.0
23 TraesCS2D01G221100 chr3D 94.059 303 17 1 1 302 248622234 248621932 2.230000e-125 459.0
24 TraesCS2D01G221100 chr1A 93.770 305 15 4 1 302 292664344 292664647 2.880000e-124 455.0
25 TraesCS2D01G221100 chr1A 83.486 109 16 2 412 519 55696154 55696047 1.560000e-17 100.0
26 TraesCS2D01G221100 chr4D 93.729 303 18 1 1 302 163789816 163790118 1.040000e-123 453.0
27 TraesCS2D01G221100 chr6B 74.832 298 61 14 407 700 229008311 229008024 3.320000e-24 122.0


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 TraesCS2D01G221100 chr2D 188551662 188554120 2458 True 4542 4542 100.000 1 2459 1 chr2D.!!$R1 2458
1 TraesCS2D01G221100 chr2B 244869480 244871640 2160 True 3310 3310 94.373 304 2459 1 chr2B.!!$R1 2155
2 TraesCS2D01G221100 chr2A 202105057 202107238 2181 True 3175 3175 93.154 303 2459 1 chr2A.!!$R1 2156
3 TraesCS2D01G221100 chr2A 202838777 202840212 1435 True 2287 2287 95.420 303 1738 1 chr2A.!!$R2 1435
4 TraesCS2D01G221100 chr7A 584395685 584396464 779 True 787 787 85.115 1685 2459 1 chr7A.!!$R2 774
5 TraesCS2D01G221100 chr7A 667941854 667942613 759 True 763 763 85.020 1709 2459 1 chr7A.!!$R3 750
6 TraesCS2D01G221100 chr6D 13032575 13033352 777 True 760 760 84.447 1688 2457 1 chr6D.!!$R1 769
7 TraesCS2D01G221100 chr7D 538240861 538241640 779 True 758 758 84.399 1687 2459 1 chr7D.!!$R1 772
8 TraesCS2D01G221100 chr7D 625028438 625029204 766 True 741 741 84.306 1685 2446 1 chr7D.!!$R2 761
9 TraesCS2D01G221100 chr5D 546676852 546677625 773 False 758 758 84.685 1699 2459 1 chr5D.!!$F3 760
10 TraesCS2D01G221100 chr3B 228692185 228692882 697 False 658 658 84.000 1749 2435 1 chr3B.!!$F1 686
11 TraesCS2D01G221100 chr4A 437496041 437496816 775 False 632 632 81.586 1686 2457 1 chr4A.!!$F1 771
12 TraesCS2D01G221100 chr1D 391244405 391245138 733 True 632 632 82.507 1690 2444 1 chr1D.!!$R1 754

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
34 35 0.250684 TGGTGCTCCATCAAAGCGAA 60.251 50.0 2.64 0.0 42.83 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1742 2.444256 GCAGAGGCCGGGGTAATCT 61.444 63.158 2.18 0.0 0.0 2.4 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 2.297701 ACATGGATAAACGGATGGTGC 58.702 47.619 0.00 0.00 0.00 5.01
21 22 2.092429 ACATGGATAAACGGATGGTGCT 60.092 45.455 0.00 0.00 0.00 4.40
22 23 2.325583 TGGATAAACGGATGGTGCTC 57.674 50.000 0.00 0.00 0.00 4.26
23 24 1.134220 TGGATAAACGGATGGTGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
32 33 3.985877 TGGTGCTCCATCAAAGCG 58.014 55.556 2.64 0.00 42.83 4.68
33 34 1.374568 TGGTGCTCCATCAAAGCGA 59.625 52.632 2.64 0.00 42.83 4.93
34 35 0.250684 TGGTGCTCCATCAAAGCGAA 60.251 50.000 2.64 0.00 42.83 4.70
35 36 0.449388 GGTGCTCCATCAAAGCGAAG 59.551 55.000 0.00 0.00 42.83 3.79
36 37 0.449388 GTGCTCCATCAAAGCGAAGG 59.551 55.000 0.00 0.00 42.83 3.46
37 38 0.324614 TGCTCCATCAAAGCGAAGGA 59.675 50.000 0.00 0.00 42.83 3.36
38 39 1.271325 TGCTCCATCAAAGCGAAGGAA 60.271 47.619 0.00 0.00 40.92 3.36
39 40 1.812571 GCTCCATCAAAGCGAAGGAAA 59.187 47.619 0.00 0.00 40.92 3.13
40 41 2.159462 GCTCCATCAAAGCGAAGGAAAG 60.159 50.000 0.00 0.00 40.92 2.62
41 42 2.421424 CTCCATCAAAGCGAAGGAAAGG 59.579 50.000 0.00 0.00 40.92 3.11
42 43 2.162681 CCATCAAAGCGAAGGAAAGGT 58.837 47.619 0.00 0.00 34.14 3.50
43 44 2.095059 CCATCAAAGCGAAGGAAAGGTG 60.095 50.000 0.00 0.00 34.14 4.00
44 45 1.604604 TCAAAGCGAAGGAAAGGTGG 58.395 50.000 0.00 0.00 0.00 4.61
45 46 1.133915 TCAAAGCGAAGGAAAGGTGGT 60.134 47.619 0.00 0.00 0.00 4.16
46 47 1.001378 CAAAGCGAAGGAAAGGTGGTG 60.001 52.381 0.00 0.00 0.00 4.17
47 48 1.172812 AAGCGAAGGAAAGGTGGTGC 61.173 55.000 0.00 0.00 0.00 5.01
48 49 1.896660 GCGAAGGAAAGGTGGTGCA 60.897 57.895 0.00 0.00 0.00 4.57
49 50 1.452145 GCGAAGGAAAGGTGGTGCAA 61.452 55.000 0.00 0.00 0.00 4.08
50 51 1.028905 CGAAGGAAAGGTGGTGCAAA 58.971 50.000 0.00 0.00 0.00 3.68
51 52 1.001378 CGAAGGAAAGGTGGTGCAAAG 60.001 52.381 0.00 0.00 0.00 2.77
52 53 1.341209 GAAGGAAAGGTGGTGCAAAGG 59.659 52.381 0.00 0.00 0.00 3.11
53 54 0.555769 AGGAAAGGTGGTGCAAAGGA 59.444 50.000 0.00 0.00 0.00 3.36
54 55 1.063266 AGGAAAGGTGGTGCAAAGGAA 60.063 47.619 0.00 0.00 0.00 3.36
55 56 1.068588 GGAAAGGTGGTGCAAAGGAAC 59.931 52.381 0.00 0.00 0.00 3.62
56 57 1.754226 GAAAGGTGGTGCAAAGGAACA 59.246 47.619 0.00 0.00 0.00 3.18
57 58 1.402787 AAGGTGGTGCAAAGGAACAG 58.597 50.000 0.00 0.00 0.00 3.16
58 59 0.550914 AGGTGGTGCAAAGGAACAGA 59.449 50.000 0.00 0.00 0.00 3.41
59 60 1.145738 AGGTGGTGCAAAGGAACAGAT 59.854 47.619 0.00 0.00 0.00 2.90
60 61 1.270550 GGTGGTGCAAAGGAACAGATG 59.729 52.381 0.00 0.00 0.00 2.90
61 62 1.956477 GTGGTGCAAAGGAACAGATGT 59.044 47.619 0.00 0.00 0.00 3.06
62 63 1.955778 TGGTGCAAAGGAACAGATGTG 59.044 47.619 0.00 0.00 0.00 3.21
63 64 1.956477 GGTGCAAAGGAACAGATGTGT 59.044 47.619 0.00 0.00 39.19 3.72
64 65 3.146066 GGTGCAAAGGAACAGATGTGTA 58.854 45.455 0.00 0.00 35.08 2.90
65 66 3.058224 GGTGCAAAGGAACAGATGTGTAC 60.058 47.826 0.00 0.00 35.08 2.90
66 67 2.805671 TGCAAAGGAACAGATGTGTACG 59.194 45.455 0.00 0.00 35.08 3.67
67 68 2.806244 GCAAAGGAACAGATGTGTACGT 59.194 45.455 0.00 0.00 35.08 3.57
68 69 3.363970 GCAAAGGAACAGATGTGTACGTG 60.364 47.826 0.00 0.00 35.08 4.49
69 70 3.746045 AAGGAACAGATGTGTACGTGT 57.254 42.857 0.00 0.00 35.08 4.49
70 71 3.746045 AGGAACAGATGTGTACGTGTT 57.254 42.857 0.00 0.00 35.08 3.32
71 72 3.390135 AGGAACAGATGTGTACGTGTTG 58.610 45.455 0.00 0.00 35.08 3.33
72 73 3.069016 AGGAACAGATGTGTACGTGTTGA 59.931 43.478 0.00 0.00 35.08 3.18
73 74 3.994392 GGAACAGATGTGTACGTGTTGAT 59.006 43.478 0.00 0.00 35.08 2.57
74 75 4.451096 GGAACAGATGTGTACGTGTTGATT 59.549 41.667 0.00 0.00 35.08 2.57
75 76 5.389516 GGAACAGATGTGTACGTGTTGATTC 60.390 44.000 0.00 0.00 35.08 2.52
76 77 3.994392 ACAGATGTGTACGTGTTGATTCC 59.006 43.478 0.00 0.00 34.05 3.01
77 78 3.993736 CAGATGTGTACGTGTTGATTCCA 59.006 43.478 0.00 0.00 0.00 3.53
78 79 3.994392 AGATGTGTACGTGTTGATTCCAC 59.006 43.478 0.00 0.00 0.00 4.02
79 80 2.485903 TGTGTACGTGTTGATTCCACC 58.514 47.619 0.00 0.00 0.00 4.61
80 81 2.103432 TGTGTACGTGTTGATTCCACCT 59.897 45.455 0.00 0.00 0.00 4.00
81 82 3.135994 GTGTACGTGTTGATTCCACCTT 58.864 45.455 0.00 0.00 0.00 3.50
82 83 4.202233 TGTGTACGTGTTGATTCCACCTTA 60.202 41.667 0.00 0.00 0.00 2.69
83 84 4.751098 GTGTACGTGTTGATTCCACCTTAA 59.249 41.667 0.00 0.00 0.00 1.85
84 85 5.236911 GTGTACGTGTTGATTCCACCTTAAA 59.763 40.000 0.00 0.00 0.00 1.52
85 86 4.823790 ACGTGTTGATTCCACCTTAAAC 57.176 40.909 0.00 0.00 0.00 2.01
86 87 4.457466 ACGTGTTGATTCCACCTTAAACT 58.543 39.130 0.00 0.00 0.00 2.66
87 88 4.885325 ACGTGTTGATTCCACCTTAAACTT 59.115 37.500 0.00 0.00 0.00 2.66
88 89 5.358725 ACGTGTTGATTCCACCTTAAACTTT 59.641 36.000 0.00 0.00 0.00 2.66
89 90 6.127563 ACGTGTTGATTCCACCTTAAACTTTT 60.128 34.615 0.00 0.00 0.00 2.27
90 91 6.754675 CGTGTTGATTCCACCTTAAACTTTTT 59.245 34.615 0.00 0.00 0.00 1.94
91 92 7.916450 CGTGTTGATTCCACCTTAAACTTTTTA 59.084 33.333 0.00 0.00 0.00 1.52
92 93 9.589111 GTGTTGATTCCACCTTAAACTTTTTAA 57.411 29.630 0.00 0.00 0.00 1.52
95 96 8.880878 TGATTCCACCTTAAACTTTTTAAAGC 57.119 30.769 2.23 0.00 39.63 3.51
96 97 7.650104 TGATTCCACCTTAAACTTTTTAAAGCG 59.350 33.333 2.23 0.00 39.63 4.68
97 98 5.834169 TCCACCTTAAACTTTTTAAAGCGG 58.166 37.500 2.23 0.00 39.63 5.52
98 99 5.593502 TCCACCTTAAACTTTTTAAAGCGGA 59.406 36.000 2.23 0.00 39.63 5.54
99 100 5.688621 CCACCTTAAACTTTTTAAAGCGGAC 59.311 40.000 2.23 0.00 39.63 4.79
100 101 5.688621 CACCTTAAACTTTTTAAAGCGGACC 59.311 40.000 2.23 0.00 39.63 4.46
101 102 5.221303 ACCTTAAACTTTTTAAAGCGGACCC 60.221 40.000 2.23 0.00 39.63 4.46
102 103 3.738830 AAACTTTTTAAAGCGGACCCC 57.261 42.857 2.23 0.00 39.63 4.95
103 104 1.624336 ACTTTTTAAAGCGGACCCCC 58.376 50.000 2.23 0.00 39.63 5.40
104 105 1.146359 ACTTTTTAAAGCGGACCCCCT 59.854 47.619 2.23 0.00 39.63 4.79
105 106 1.816835 CTTTTTAAAGCGGACCCCCTC 59.183 52.381 0.00 0.00 0.00 4.30
106 107 1.069775 TTTTAAAGCGGACCCCCTCT 58.930 50.000 0.00 0.00 0.00 3.69
107 108 1.069775 TTTAAAGCGGACCCCCTCTT 58.930 50.000 0.00 0.00 39.06 2.85
108 109 1.955451 TTAAAGCGGACCCCCTCTTA 58.045 50.000 0.00 0.00 36.53 2.10
109 110 1.955451 TAAAGCGGACCCCCTCTTAA 58.045 50.000 0.00 0.00 36.53 1.85
110 111 1.296002 AAAGCGGACCCCCTCTTAAT 58.704 50.000 0.00 0.00 36.53 1.40
111 112 2.185663 AAGCGGACCCCCTCTTAATA 57.814 50.000 0.00 0.00 35.83 0.98
112 113 1.718280 AGCGGACCCCCTCTTAATAG 58.282 55.000 0.00 0.00 0.00 1.73
113 114 1.062352 AGCGGACCCCCTCTTAATAGT 60.062 52.381 0.00 0.00 0.00 2.12
114 115 2.178544 AGCGGACCCCCTCTTAATAGTA 59.821 50.000 0.00 0.00 0.00 1.82
115 116 2.298446 GCGGACCCCCTCTTAATAGTAC 59.702 54.545 0.00 0.00 0.00 2.73
116 117 2.555757 CGGACCCCCTCTTAATAGTACG 59.444 54.545 0.00 0.00 0.00 3.67
117 118 2.896044 GGACCCCCTCTTAATAGTACGG 59.104 54.545 0.00 0.00 0.00 4.02
118 119 2.298446 GACCCCCTCTTAATAGTACGGC 59.702 54.545 0.00 0.00 0.00 5.68
119 120 2.090887 ACCCCCTCTTAATAGTACGGCT 60.091 50.000 0.00 0.00 0.00 5.52
120 121 2.970640 CCCCCTCTTAATAGTACGGCTT 59.029 50.000 0.00 0.00 0.00 4.35
121 122 3.390311 CCCCCTCTTAATAGTACGGCTTT 59.610 47.826 0.00 0.00 0.00 3.51
122 123 4.502777 CCCCCTCTTAATAGTACGGCTTTC 60.503 50.000 0.00 0.00 0.00 2.62
123 124 4.502777 CCCCTCTTAATAGTACGGCTTTCC 60.503 50.000 0.00 0.00 0.00 3.13
124 125 4.344390 CCCTCTTAATAGTACGGCTTTCCT 59.656 45.833 0.00 0.00 0.00 3.36
125 126 5.537674 CCCTCTTAATAGTACGGCTTTCCTA 59.462 44.000 0.00 0.00 0.00 2.94
126 127 6.445475 CCTCTTAATAGTACGGCTTTCCTAC 58.555 44.000 0.00 0.00 0.00 3.18
127 128 6.064846 TCTTAATAGTACGGCTTTCCTACG 57.935 41.667 0.00 0.00 0.00 3.51
128 129 5.822519 TCTTAATAGTACGGCTTTCCTACGA 59.177 40.000 0.00 0.00 0.00 3.43
129 130 3.978718 ATAGTACGGCTTTCCTACGAC 57.021 47.619 0.00 0.00 0.00 4.34
130 131 1.831580 AGTACGGCTTTCCTACGACT 58.168 50.000 0.00 0.00 0.00 4.18
131 132 1.742268 AGTACGGCTTTCCTACGACTC 59.258 52.381 0.00 0.00 0.00 3.36
132 133 1.470098 GTACGGCTTTCCTACGACTCA 59.530 52.381 0.00 0.00 0.00 3.41
133 134 0.963962 ACGGCTTTCCTACGACTCAA 59.036 50.000 0.00 0.00 0.00 3.02
134 135 1.549170 ACGGCTTTCCTACGACTCAAT 59.451 47.619 0.00 0.00 0.00 2.57
135 136 2.028385 ACGGCTTTCCTACGACTCAATT 60.028 45.455 0.00 0.00 0.00 2.32
136 137 2.603560 CGGCTTTCCTACGACTCAATTC 59.396 50.000 0.00 0.00 0.00 2.17
137 138 2.937149 GGCTTTCCTACGACTCAATTCC 59.063 50.000 0.00 0.00 0.00 3.01
138 139 3.596214 GCTTTCCTACGACTCAATTCCA 58.404 45.455 0.00 0.00 0.00 3.53
139 140 3.371285 GCTTTCCTACGACTCAATTCCAC 59.629 47.826 0.00 0.00 0.00 4.02
140 141 3.604875 TTCCTACGACTCAATTCCACC 57.395 47.619 0.00 0.00 0.00 4.61
141 142 1.475280 TCCTACGACTCAATTCCACCG 59.525 52.381 0.00 0.00 0.00 4.94
142 143 1.475280 CCTACGACTCAATTCCACCGA 59.525 52.381 0.00 0.00 0.00 4.69
143 144 2.094390 CCTACGACTCAATTCCACCGAA 60.094 50.000 0.00 0.00 0.00 4.30
144 145 2.536761 ACGACTCAATTCCACCGAAA 57.463 45.000 0.00 0.00 0.00 3.46
145 146 2.841215 ACGACTCAATTCCACCGAAAA 58.159 42.857 0.00 0.00 0.00 2.29
146 147 2.806244 ACGACTCAATTCCACCGAAAAG 59.194 45.455 0.00 0.00 0.00 2.27
147 148 3.064207 CGACTCAATTCCACCGAAAAGA 58.936 45.455 0.00 0.00 0.00 2.52
148 149 3.496884 CGACTCAATTCCACCGAAAAGAA 59.503 43.478 0.00 0.00 0.00 2.52
149 150 4.024387 CGACTCAATTCCACCGAAAAGAAA 60.024 41.667 0.00 0.00 0.00 2.52
150 151 5.334879 CGACTCAATTCCACCGAAAAGAAAT 60.335 40.000 0.00 0.00 0.00 2.17
151 152 5.772521 ACTCAATTCCACCGAAAAGAAATG 58.227 37.500 0.00 0.00 0.00 2.32
152 153 5.534654 ACTCAATTCCACCGAAAAGAAATGA 59.465 36.000 0.00 0.00 30.77 2.57
153 154 6.040391 ACTCAATTCCACCGAAAAGAAATGAA 59.960 34.615 0.00 0.00 31.08 2.57
154 155 6.446318 TCAATTCCACCGAAAAGAAATGAAG 58.554 36.000 0.00 0.00 28.98 3.02
155 156 6.264292 TCAATTCCACCGAAAAGAAATGAAGA 59.736 34.615 0.00 0.00 28.98 2.87
156 157 5.689383 TTCCACCGAAAAGAAATGAAGAG 57.311 39.130 0.00 0.00 0.00 2.85
157 158 4.968259 TCCACCGAAAAGAAATGAAGAGA 58.032 39.130 0.00 0.00 0.00 3.10
158 159 5.373222 TCCACCGAAAAGAAATGAAGAGAA 58.627 37.500 0.00 0.00 0.00 2.87
159 160 5.238650 TCCACCGAAAAGAAATGAAGAGAAC 59.761 40.000 0.00 0.00 0.00 3.01
160 161 5.008613 CCACCGAAAAGAAATGAAGAGAACA 59.991 40.000 0.00 0.00 0.00 3.18
161 162 6.138761 CACCGAAAAGAAATGAAGAGAACAG 58.861 40.000 0.00 0.00 0.00 3.16
162 163 5.149977 CCGAAAAGAAATGAAGAGAACAGC 58.850 41.667 0.00 0.00 0.00 4.40
163 164 5.149977 CGAAAAGAAATGAAGAGAACAGCC 58.850 41.667 0.00 0.00 0.00 4.85
164 165 5.277974 CGAAAAGAAATGAAGAGAACAGCCA 60.278 40.000 0.00 0.00 0.00 4.75
165 166 6.569226 CGAAAAGAAATGAAGAGAACAGCCAT 60.569 38.462 0.00 0.00 0.00 4.40
166 167 5.893897 AAGAAATGAAGAGAACAGCCATC 57.106 39.130 0.00 0.00 0.00 3.51
167 168 5.176741 AGAAATGAAGAGAACAGCCATCT 57.823 39.130 0.00 0.00 0.00 2.90
168 169 5.568392 AGAAATGAAGAGAACAGCCATCTT 58.432 37.500 0.00 0.00 36.02 2.40
169 170 5.647225 AGAAATGAAGAGAACAGCCATCTTC 59.353 40.000 7.12 7.12 45.92 2.87
171 172 3.238108 GAAGAGAACAGCCATCTTCGA 57.762 47.619 0.00 0.00 39.51 3.71
172 173 3.791245 GAAGAGAACAGCCATCTTCGAT 58.209 45.455 0.00 0.00 39.51 3.59
173 174 4.938080 GAAGAGAACAGCCATCTTCGATA 58.062 43.478 0.00 0.00 39.51 2.92
174 175 4.582701 AGAGAACAGCCATCTTCGATAG 57.417 45.455 0.00 0.00 0.00 2.08
175 176 3.320541 AGAGAACAGCCATCTTCGATAGG 59.679 47.826 0.00 0.00 0.00 2.57
179 180 3.523806 GCCATCTTCGATAGGCTCC 57.476 57.895 9.77 0.00 43.70 4.70
180 181 0.389166 GCCATCTTCGATAGGCTCCG 60.389 60.000 9.77 0.00 43.70 4.63
181 182 1.248486 CCATCTTCGATAGGCTCCGA 58.752 55.000 7.67 7.67 0.00 4.55
182 183 1.201181 CCATCTTCGATAGGCTCCGAG 59.799 57.143 10.92 0.00 36.11 4.63
183 184 1.201181 CATCTTCGATAGGCTCCGAGG 59.799 57.143 12.80 12.80 36.11 4.63
184 185 0.537600 TCTTCGATAGGCTCCGAGGG 60.538 60.000 16.87 11.88 36.11 4.30
185 186 1.528292 CTTCGATAGGCTCCGAGGGG 61.528 65.000 11.64 0.00 36.11 4.79
186 187 3.686045 CGATAGGCTCCGAGGGGC 61.686 72.222 5.20 5.20 0.00 5.80
187 188 2.524394 GATAGGCTCCGAGGGGCA 60.524 66.667 16.68 0.00 0.00 5.36
188 189 2.844839 ATAGGCTCCGAGGGGCAC 60.845 66.667 16.68 5.38 0.00 5.01
201 202 2.471255 GGGCACCGAATCTCTTGTG 58.529 57.895 0.00 0.00 40.86 3.33
203 204 1.796796 GCACCGAATCTCTTGTGCC 59.203 57.895 2.19 0.00 46.33 5.01
204 205 0.674895 GCACCGAATCTCTTGTGCCT 60.675 55.000 2.19 0.00 46.33 4.75
205 206 1.405526 GCACCGAATCTCTTGTGCCTA 60.406 52.381 2.19 0.00 46.33 3.93
206 207 2.544685 CACCGAATCTCTTGTGCCTAG 58.455 52.381 0.00 0.00 0.00 3.02
207 208 2.166459 CACCGAATCTCTTGTGCCTAGA 59.834 50.000 0.00 0.00 0.00 2.43
208 209 2.166664 ACCGAATCTCTTGTGCCTAGAC 59.833 50.000 0.00 0.00 0.00 2.59
209 210 2.166459 CCGAATCTCTTGTGCCTAGACA 59.834 50.000 0.00 0.00 0.00 3.41
210 211 3.181471 CCGAATCTCTTGTGCCTAGACAT 60.181 47.826 0.00 0.00 0.00 3.06
211 212 3.801050 CGAATCTCTTGTGCCTAGACATG 59.199 47.826 0.00 0.00 0.00 3.21
212 213 4.440663 CGAATCTCTTGTGCCTAGACATGA 60.441 45.833 0.00 0.00 0.00 3.07
213 214 4.669206 ATCTCTTGTGCCTAGACATGAG 57.331 45.455 15.83 15.83 44.10 2.90
214 215 3.701664 TCTCTTGTGCCTAGACATGAGA 58.298 45.455 18.64 18.64 46.73 3.27
215 216 4.285020 TCTCTTGTGCCTAGACATGAGAT 58.715 43.478 18.64 0.00 45.31 2.75
216 217 5.449553 TCTCTTGTGCCTAGACATGAGATA 58.550 41.667 18.64 5.83 45.31 1.98
217 218 6.073981 TCTCTTGTGCCTAGACATGAGATAT 58.926 40.000 18.64 0.00 45.31 1.63
218 219 6.208402 TCTCTTGTGCCTAGACATGAGATATC 59.792 42.308 18.64 0.00 45.31 1.63
219 220 6.073981 TCTTGTGCCTAGACATGAGATATCT 58.926 40.000 4.47 4.47 0.00 1.98
220 221 5.718724 TGTGCCTAGACATGAGATATCTG 57.281 43.478 10.74 0.00 0.00 2.90
221 222 5.388654 TGTGCCTAGACATGAGATATCTGA 58.611 41.667 10.74 1.00 0.00 3.27
222 223 5.835280 TGTGCCTAGACATGAGATATCTGAA 59.165 40.000 10.74 0.00 0.00 3.02
223 224 6.324770 TGTGCCTAGACATGAGATATCTGAAA 59.675 38.462 10.74 0.00 0.00 2.69
224 225 7.015974 TGTGCCTAGACATGAGATATCTGAAAT 59.984 37.037 10.74 0.00 0.00 2.17
225 226 7.331440 GTGCCTAGACATGAGATATCTGAAATG 59.669 40.741 10.74 12.92 0.00 2.32
226 227 6.313411 GCCTAGACATGAGATATCTGAAATGC 59.687 42.308 10.74 7.65 0.00 3.56
227 228 7.613585 CCTAGACATGAGATATCTGAAATGCT 58.386 38.462 10.74 13.19 0.00 3.79
228 229 7.760794 CCTAGACATGAGATATCTGAAATGCTC 59.239 40.741 10.74 10.50 0.00 4.26
229 230 7.063934 AGACATGAGATATCTGAAATGCTCA 57.936 36.000 10.74 0.00 36.88 4.26
230 231 7.506971 AGACATGAGATATCTGAAATGCTCAA 58.493 34.615 10.74 0.00 36.17 3.02
231 232 8.158132 AGACATGAGATATCTGAAATGCTCAAT 58.842 33.333 10.74 0.00 36.17 2.57
232 233 8.100508 ACATGAGATATCTGAAATGCTCAATG 57.899 34.615 10.74 0.00 36.17 2.82
233 234 6.555812 TGAGATATCTGAAATGCTCAATGC 57.444 37.500 10.74 0.00 43.25 3.56
245 246 3.310303 GCTCAATGCACACGATTAGTC 57.690 47.619 0.00 0.00 42.31 2.59
246 247 2.932614 GCTCAATGCACACGATTAGTCT 59.067 45.455 0.00 0.00 42.31 3.24
247 248 3.242220 GCTCAATGCACACGATTAGTCTG 60.242 47.826 0.00 0.00 42.31 3.51
248 249 2.672874 TCAATGCACACGATTAGTCTGC 59.327 45.455 0.00 0.00 43.73 4.26
252 253 3.747099 GCACACGATTAGTCTGCAAAT 57.253 42.857 0.00 0.00 43.09 2.32
253 254 3.419915 GCACACGATTAGTCTGCAAATG 58.580 45.455 0.00 0.00 43.09 2.32
254 255 3.419915 CACACGATTAGTCTGCAAATGC 58.580 45.455 0.00 0.00 42.50 3.56
268 269 3.327626 GCAAATGCATTGTCACCAATCA 58.672 40.909 13.82 0.00 39.28 2.57
269 270 3.123959 GCAAATGCATTGTCACCAATCAC 59.876 43.478 13.82 0.00 39.28 3.06
270 271 3.598019 AATGCATTGTCACCAATCACC 57.402 42.857 12.09 0.00 39.28 4.02
271 272 1.992538 TGCATTGTCACCAATCACCA 58.007 45.000 0.00 0.00 39.28 4.17
272 273 2.314246 TGCATTGTCACCAATCACCAA 58.686 42.857 0.00 0.00 39.28 3.67
273 274 2.697229 TGCATTGTCACCAATCACCAAA 59.303 40.909 0.00 0.00 39.28 3.28
274 275 3.133542 TGCATTGTCACCAATCACCAAAA 59.866 39.130 0.00 0.00 39.28 2.44
275 276 3.494251 GCATTGTCACCAATCACCAAAAC 59.506 43.478 0.00 0.00 39.28 2.43
276 277 3.810310 TTGTCACCAATCACCAAAACC 57.190 42.857 0.00 0.00 0.00 3.27
277 278 2.739943 TGTCACCAATCACCAAAACCA 58.260 42.857 0.00 0.00 0.00 3.67
278 279 2.428890 TGTCACCAATCACCAAAACCAC 59.571 45.455 0.00 0.00 0.00 4.16
279 280 2.693074 GTCACCAATCACCAAAACCACT 59.307 45.455 0.00 0.00 0.00 4.00
280 281 3.132111 GTCACCAATCACCAAAACCACTT 59.868 43.478 0.00 0.00 0.00 3.16
281 282 4.339814 GTCACCAATCACCAAAACCACTTA 59.660 41.667 0.00 0.00 0.00 2.24
282 283 4.582656 TCACCAATCACCAAAACCACTTAG 59.417 41.667 0.00 0.00 0.00 2.18
283 284 3.895041 ACCAATCACCAAAACCACTTAGG 59.105 43.478 0.00 0.00 45.67 2.69
284 285 3.258123 CCAATCACCAAAACCACTTAGGG 59.742 47.826 0.00 0.00 43.89 3.53
285 286 4.148838 CAATCACCAAAACCACTTAGGGA 58.851 43.478 0.00 0.00 43.89 4.20
286 287 3.502123 TCACCAAAACCACTTAGGGAG 57.498 47.619 0.00 0.00 43.89 4.30
287 288 3.050089 TCACCAAAACCACTTAGGGAGA 58.950 45.455 0.00 0.00 43.89 3.71
288 289 3.460340 TCACCAAAACCACTTAGGGAGAA 59.540 43.478 0.00 0.00 43.89 2.87
289 290 4.079672 TCACCAAAACCACTTAGGGAGAAA 60.080 41.667 0.00 0.00 43.89 2.52
290 291 4.832823 CACCAAAACCACTTAGGGAGAAAT 59.167 41.667 0.00 0.00 43.89 2.17
291 292 6.007703 CACCAAAACCACTTAGGGAGAAATA 58.992 40.000 0.00 0.00 43.89 1.40
292 293 6.663523 CACCAAAACCACTTAGGGAGAAATAT 59.336 38.462 0.00 0.00 43.89 1.28
293 294 6.663523 ACCAAAACCACTTAGGGAGAAATATG 59.336 38.462 0.00 0.00 43.89 1.78
294 295 6.405842 CCAAAACCACTTAGGGAGAAATATGC 60.406 42.308 0.00 0.00 43.89 3.14
295 296 4.439253 ACCACTTAGGGAGAAATATGCC 57.561 45.455 0.00 0.00 43.89 4.40
296 297 3.138468 ACCACTTAGGGAGAAATATGCCC 59.862 47.826 0.00 0.00 43.89 5.36
419 420 4.822350 GGTTGCTAGAGTTTGTTTCTCCTT 59.178 41.667 0.00 0.00 32.93 3.36
431 432 7.286316 AGTTTGTTTCTCCTTGTCATTCTGAAT 59.714 33.333 0.00 0.00 0.00 2.57
526 527 6.469782 AATGATATGCGGAGGTTGAAATTT 57.530 33.333 0.00 0.00 0.00 1.82
528 529 6.618287 TGATATGCGGAGGTTGAAATTTAG 57.382 37.500 0.00 0.00 0.00 1.85
534 535 4.083696 GCGGAGGTTGAAATTTAGTCGAAA 60.084 41.667 0.00 0.00 0.00 3.46
653 654 2.917933 TGCGGAAGTGAAAGATATGGG 58.082 47.619 0.00 0.00 0.00 4.00
1063 1096 2.821969 CTGGTGCTTGGATGCTTTACTT 59.178 45.455 0.00 0.00 0.00 2.24
1083 1116 6.882610 ACTTCTCATGCAAATTGTAAGTGA 57.117 33.333 0.00 0.00 0.00 3.41
1121 1154 8.405531 GCAGCCAAGTCATTACTTATAATTTCA 58.594 33.333 0.00 0.00 44.28 2.69
1228 1262 2.316792 CGAGAACTCGTTGGTACAGTG 58.683 52.381 14.87 0.00 46.99 3.66
1587 1625 6.430308 TGTGGTTTATTACGCCTCAACAAATA 59.570 34.615 0.00 0.00 0.00 1.40
1639 1677 0.468226 AACTCAAGTGCTTCGACCCA 59.532 50.000 0.00 0.00 0.00 4.51
2049 2096 1.367840 GAGACCAGACAACGCCACT 59.632 57.895 0.00 0.00 0.00 4.00
2138 2192 2.665649 ATGCGGTCGATGAAACACTA 57.334 45.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.092429 AGCACCATCCGTTTATCCATGT 60.092 45.455 0.00 0.00 0.00 3.21
1 2 2.549754 GAGCACCATCCGTTTATCCATG 59.450 50.000 0.00 0.00 0.00 3.66
2 3 2.487265 GGAGCACCATCCGTTTATCCAT 60.487 50.000 0.00 0.00 35.97 3.41
4 5 1.134220 TGGAGCACCATCCGTTTATCC 60.134 52.381 0.00 0.00 42.77 2.59
5 6 2.325583 TGGAGCACCATCCGTTTATC 57.674 50.000 0.00 0.00 42.77 1.75
16 17 0.449388 CTTCGCTTTGATGGAGCACC 59.551 55.000 0.00 0.00 40.13 5.01
17 18 0.449388 CCTTCGCTTTGATGGAGCAC 59.551 55.000 0.00 0.00 43.07 4.40
18 19 0.324614 TCCTTCGCTTTGATGGAGCA 59.675 50.000 0.00 0.00 43.87 4.26
19 20 3.159298 TCCTTCGCTTTGATGGAGC 57.841 52.632 0.00 0.00 43.87 4.70
21 22 2.224769 ACCTTTCCTTCGCTTTGATGGA 60.225 45.455 0.00 0.00 46.25 3.41
22 23 2.095059 CACCTTTCCTTCGCTTTGATGG 60.095 50.000 0.00 0.00 42.05 3.51
23 24 2.095059 CCACCTTTCCTTCGCTTTGATG 60.095 50.000 0.00 0.00 0.00 3.07
24 25 2.162681 CCACCTTTCCTTCGCTTTGAT 58.837 47.619 0.00 0.00 0.00 2.57
25 26 1.133915 ACCACCTTTCCTTCGCTTTGA 60.134 47.619 0.00 0.00 0.00 2.69
26 27 1.001378 CACCACCTTTCCTTCGCTTTG 60.001 52.381 0.00 0.00 0.00 2.77
27 28 1.318576 CACCACCTTTCCTTCGCTTT 58.681 50.000 0.00 0.00 0.00 3.51
28 29 1.172812 GCACCACCTTTCCTTCGCTT 61.173 55.000 0.00 0.00 0.00 4.68
29 30 1.600916 GCACCACCTTTCCTTCGCT 60.601 57.895 0.00 0.00 0.00 4.93
30 31 1.452145 TTGCACCACCTTTCCTTCGC 61.452 55.000 0.00 0.00 0.00 4.70
31 32 1.001378 CTTTGCACCACCTTTCCTTCG 60.001 52.381 0.00 0.00 0.00 3.79
32 33 1.341209 CCTTTGCACCACCTTTCCTTC 59.659 52.381 0.00 0.00 0.00 3.46
33 34 1.063266 TCCTTTGCACCACCTTTCCTT 60.063 47.619 0.00 0.00 0.00 3.36
34 35 0.555769 TCCTTTGCACCACCTTTCCT 59.444 50.000 0.00 0.00 0.00 3.36
35 36 1.068588 GTTCCTTTGCACCACCTTTCC 59.931 52.381 0.00 0.00 0.00 3.13
36 37 1.754226 TGTTCCTTTGCACCACCTTTC 59.246 47.619 0.00 0.00 0.00 2.62
37 38 1.756538 CTGTTCCTTTGCACCACCTTT 59.243 47.619 0.00 0.00 0.00 3.11
38 39 1.064017 TCTGTTCCTTTGCACCACCTT 60.064 47.619 0.00 0.00 0.00 3.50
39 40 0.550914 TCTGTTCCTTTGCACCACCT 59.449 50.000 0.00 0.00 0.00 4.00
40 41 1.270550 CATCTGTTCCTTTGCACCACC 59.729 52.381 0.00 0.00 0.00 4.61
41 42 1.956477 ACATCTGTTCCTTTGCACCAC 59.044 47.619 0.00 0.00 0.00 4.16
42 43 1.955778 CACATCTGTTCCTTTGCACCA 59.044 47.619 0.00 0.00 0.00 4.17
43 44 1.956477 ACACATCTGTTCCTTTGCACC 59.044 47.619 0.00 0.00 0.00 5.01
44 45 3.363970 CGTACACATCTGTTCCTTTGCAC 60.364 47.826 0.00 0.00 0.00 4.57
45 46 2.805671 CGTACACATCTGTTCCTTTGCA 59.194 45.455 0.00 0.00 0.00 4.08
46 47 2.806244 ACGTACACATCTGTTCCTTTGC 59.194 45.455 0.00 0.00 0.00 3.68
47 48 3.807622 ACACGTACACATCTGTTCCTTTG 59.192 43.478 0.00 0.00 0.00 2.77
48 49 4.067972 ACACGTACACATCTGTTCCTTT 57.932 40.909 0.00 0.00 0.00 3.11
49 50 3.746045 ACACGTACACATCTGTTCCTT 57.254 42.857 0.00 0.00 0.00 3.36
50 51 3.069016 TCAACACGTACACATCTGTTCCT 59.931 43.478 0.00 0.00 0.00 3.36
51 52 3.386486 TCAACACGTACACATCTGTTCC 58.614 45.455 0.00 0.00 0.00 3.62
52 53 5.389516 GGAATCAACACGTACACATCTGTTC 60.390 44.000 0.00 0.00 0.00 3.18
53 54 4.451096 GGAATCAACACGTACACATCTGTT 59.549 41.667 0.00 0.00 0.00 3.16
54 55 3.994392 GGAATCAACACGTACACATCTGT 59.006 43.478 0.00 0.00 0.00 3.41
55 56 3.993736 TGGAATCAACACGTACACATCTG 59.006 43.478 0.00 0.00 0.00 2.90
56 57 3.994392 GTGGAATCAACACGTACACATCT 59.006 43.478 0.00 0.00 0.00 2.90
57 58 3.124636 GGTGGAATCAACACGTACACATC 59.875 47.826 0.00 0.00 39.69 3.06
58 59 3.071479 GGTGGAATCAACACGTACACAT 58.929 45.455 0.00 0.00 39.69 3.21
59 60 2.103432 AGGTGGAATCAACACGTACACA 59.897 45.455 0.00 0.00 39.69 3.72
60 61 2.762745 AGGTGGAATCAACACGTACAC 58.237 47.619 0.00 0.00 39.69 2.90
61 62 3.478857 AAGGTGGAATCAACACGTACA 57.521 42.857 0.00 0.00 39.69 2.90
62 63 5.467735 AGTTTAAGGTGGAATCAACACGTAC 59.532 40.000 0.00 0.00 39.69 3.67
63 64 5.613329 AGTTTAAGGTGGAATCAACACGTA 58.387 37.500 0.00 0.00 39.69 3.57
64 65 4.457466 AGTTTAAGGTGGAATCAACACGT 58.543 39.130 0.00 0.00 39.69 4.49
65 66 5.432885 AAGTTTAAGGTGGAATCAACACG 57.567 39.130 0.00 0.00 39.69 4.49
66 67 9.589111 TTAAAAAGTTTAAGGTGGAATCAACAC 57.411 29.630 0.00 0.00 38.10 3.32
69 70 9.320352 GCTTTAAAAAGTTTAAGGTGGAATCAA 57.680 29.630 4.50 0.00 38.28 2.57
70 71 7.650104 CGCTTTAAAAAGTTTAAGGTGGAATCA 59.350 33.333 4.50 0.00 38.28 2.57
71 72 7.115805 CCGCTTTAAAAAGTTTAAGGTGGAATC 59.884 37.037 21.50 0.17 41.37 2.52
72 73 6.926826 CCGCTTTAAAAAGTTTAAGGTGGAAT 59.073 34.615 21.50 0.00 41.37 3.01
73 74 6.096564 TCCGCTTTAAAAAGTTTAAGGTGGAA 59.903 34.615 24.19 14.14 43.19 3.53
74 75 5.593502 TCCGCTTTAAAAAGTTTAAGGTGGA 59.406 36.000 23.29 23.29 43.61 4.02
75 76 5.688621 GTCCGCTTTAAAAAGTTTAAGGTGG 59.311 40.000 20.63 20.63 40.69 4.61
76 77 5.688621 GGTCCGCTTTAAAAAGTTTAAGGTG 59.311 40.000 4.50 8.41 38.28 4.00
77 78 5.221303 GGGTCCGCTTTAAAAAGTTTAAGGT 60.221 40.000 4.50 0.00 38.28 3.50
78 79 5.224888 GGGTCCGCTTTAAAAAGTTTAAGG 58.775 41.667 4.50 0.00 38.28 2.69
79 80 5.224888 GGGGTCCGCTTTAAAAAGTTTAAG 58.775 41.667 0.00 0.00 38.28 1.85
80 81 4.039004 GGGGGTCCGCTTTAAAAAGTTTAA 59.961 41.667 5.82 0.00 38.28 1.52
81 82 3.573538 GGGGGTCCGCTTTAAAAAGTTTA 59.426 43.478 5.82 0.00 38.28 2.01
82 83 2.366266 GGGGGTCCGCTTTAAAAAGTTT 59.634 45.455 5.82 0.00 38.28 2.66
83 84 1.965643 GGGGGTCCGCTTTAAAAAGTT 59.034 47.619 5.82 0.00 38.28 2.66
84 85 1.146359 AGGGGGTCCGCTTTAAAAAGT 59.854 47.619 5.82 0.00 38.28 2.66
85 86 1.816835 GAGGGGGTCCGCTTTAAAAAG 59.183 52.381 8.01 0.00 39.38 2.27
86 87 1.426215 AGAGGGGGTCCGCTTTAAAAA 59.574 47.619 8.01 0.00 40.39 1.94
87 88 1.069775 AGAGGGGGTCCGCTTTAAAA 58.930 50.000 8.01 0.00 40.39 1.52
88 89 2.781631 AGAGGGGGTCCGCTTTAAA 58.218 52.632 8.01 0.00 40.39 1.52
89 90 4.573261 AGAGGGGGTCCGCTTTAA 57.427 55.556 8.01 0.00 40.39 1.52
93 94 1.062352 ACTATTAAGAGGGGGTCCGCT 60.062 52.381 6.27 6.27 45.35 5.52
94 95 1.421480 ACTATTAAGAGGGGGTCCGC 58.579 55.000 1.59 0.00 38.33 5.54
95 96 2.555757 CGTACTATTAAGAGGGGGTCCG 59.444 54.545 1.59 0.00 38.33 4.79
96 97 2.896044 CCGTACTATTAAGAGGGGGTCC 59.104 54.545 1.59 0.00 0.00 4.46
97 98 2.298446 GCCGTACTATTAAGAGGGGGTC 59.702 54.545 1.59 0.00 0.00 4.46
98 99 2.090887 AGCCGTACTATTAAGAGGGGGT 60.091 50.000 1.59 2.91 0.00 4.95
99 100 2.606378 AGCCGTACTATTAAGAGGGGG 58.394 52.381 1.59 0.99 0.00 5.40
100 101 4.502777 GGAAAGCCGTACTATTAAGAGGGG 60.503 50.000 1.59 1.33 0.00 4.79
101 102 4.344390 AGGAAAGCCGTACTATTAAGAGGG 59.656 45.833 1.59 0.00 39.96 4.30
102 103 5.532664 AGGAAAGCCGTACTATTAAGAGG 57.467 43.478 1.59 0.00 39.96 3.69
103 104 6.017605 TCGTAGGAAAGCCGTACTATTAAGAG 60.018 42.308 0.00 0.00 39.96 2.85
104 105 5.822519 TCGTAGGAAAGCCGTACTATTAAGA 59.177 40.000 0.00 0.00 39.96 2.10
105 106 5.911838 GTCGTAGGAAAGCCGTACTATTAAG 59.088 44.000 0.00 0.00 39.96 1.85
106 107 5.590259 AGTCGTAGGAAAGCCGTACTATTAA 59.410 40.000 0.00 0.00 39.96 1.40
107 108 5.126067 AGTCGTAGGAAAGCCGTACTATTA 58.874 41.667 0.00 0.00 39.96 0.98
108 109 3.950395 AGTCGTAGGAAAGCCGTACTATT 59.050 43.478 0.00 0.00 39.96 1.73
109 110 3.549794 AGTCGTAGGAAAGCCGTACTAT 58.450 45.455 0.00 0.00 39.96 2.12
110 111 2.939103 GAGTCGTAGGAAAGCCGTACTA 59.061 50.000 0.00 0.00 39.96 1.82
111 112 1.742268 GAGTCGTAGGAAAGCCGTACT 59.258 52.381 0.00 0.00 39.96 2.73
112 113 1.470098 TGAGTCGTAGGAAAGCCGTAC 59.530 52.381 0.00 0.00 39.96 3.67
113 114 1.825090 TGAGTCGTAGGAAAGCCGTA 58.175 50.000 0.00 0.00 39.96 4.02
114 115 0.963962 TTGAGTCGTAGGAAAGCCGT 59.036 50.000 0.00 0.00 39.96 5.68
115 116 2.295253 ATTGAGTCGTAGGAAAGCCG 57.705 50.000 0.00 0.00 39.96 5.52
116 117 2.937149 GGAATTGAGTCGTAGGAAAGCC 59.063 50.000 0.00 0.00 0.00 4.35
117 118 3.371285 GTGGAATTGAGTCGTAGGAAAGC 59.629 47.826 0.00 0.00 0.00 3.51
118 119 3.933332 GGTGGAATTGAGTCGTAGGAAAG 59.067 47.826 0.00 0.00 0.00 2.62
119 120 3.615592 CGGTGGAATTGAGTCGTAGGAAA 60.616 47.826 0.00 0.00 0.00 3.13
120 121 2.094390 CGGTGGAATTGAGTCGTAGGAA 60.094 50.000 0.00 0.00 0.00 3.36
121 122 1.475280 CGGTGGAATTGAGTCGTAGGA 59.525 52.381 0.00 0.00 0.00 2.94
122 123 1.475280 TCGGTGGAATTGAGTCGTAGG 59.525 52.381 0.00 0.00 0.00 3.18
123 124 2.933495 TCGGTGGAATTGAGTCGTAG 57.067 50.000 0.00 0.00 0.00 3.51
124 125 3.663995 TTTCGGTGGAATTGAGTCGTA 57.336 42.857 0.00 0.00 30.88 3.43
125 126 2.536761 TTTCGGTGGAATTGAGTCGT 57.463 45.000 0.00 0.00 30.88 4.34
126 127 3.064207 TCTTTTCGGTGGAATTGAGTCG 58.936 45.455 0.00 0.00 30.88 4.18
127 128 5.432885 TTTCTTTTCGGTGGAATTGAGTC 57.567 39.130 0.00 0.00 30.88 3.36
128 129 5.534654 TCATTTCTTTTCGGTGGAATTGAGT 59.465 36.000 0.00 0.00 30.83 3.41
129 130 6.012658 TCATTTCTTTTCGGTGGAATTGAG 57.987 37.500 0.00 0.00 30.83 3.02
130 131 6.264292 TCTTCATTTCTTTTCGGTGGAATTGA 59.736 34.615 0.00 0.00 31.77 2.57
131 132 6.446318 TCTTCATTTCTTTTCGGTGGAATTG 58.554 36.000 0.00 0.00 30.88 2.32
132 133 6.490040 TCTCTTCATTTCTTTTCGGTGGAATT 59.510 34.615 0.00 0.00 30.88 2.17
133 134 6.003950 TCTCTTCATTTCTTTTCGGTGGAAT 58.996 36.000 0.00 0.00 30.88 3.01
134 135 5.373222 TCTCTTCATTTCTTTTCGGTGGAA 58.627 37.500 0.00 0.00 0.00 3.53
135 136 4.968259 TCTCTTCATTTCTTTTCGGTGGA 58.032 39.130 0.00 0.00 0.00 4.02
136 137 5.008613 TGTTCTCTTCATTTCTTTTCGGTGG 59.991 40.000 0.00 0.00 0.00 4.61
137 138 6.060028 TGTTCTCTTCATTTCTTTTCGGTG 57.940 37.500 0.00 0.00 0.00 4.94
138 139 5.278022 GCTGTTCTCTTCATTTCTTTTCGGT 60.278 40.000 0.00 0.00 0.00 4.69
139 140 5.149977 GCTGTTCTCTTCATTTCTTTTCGG 58.850 41.667 0.00 0.00 0.00 4.30
140 141 5.149977 GGCTGTTCTCTTCATTTCTTTTCG 58.850 41.667 0.00 0.00 0.00 3.46
141 142 6.076981 TGGCTGTTCTCTTCATTTCTTTTC 57.923 37.500 0.00 0.00 0.00 2.29
142 143 6.492772 AGATGGCTGTTCTCTTCATTTCTTTT 59.507 34.615 0.00 0.00 0.00 2.27
143 144 6.008960 AGATGGCTGTTCTCTTCATTTCTTT 58.991 36.000 0.00 0.00 0.00 2.52
144 145 5.568392 AGATGGCTGTTCTCTTCATTTCTT 58.432 37.500 0.00 0.00 0.00 2.52
145 146 5.176741 AGATGGCTGTTCTCTTCATTTCT 57.823 39.130 0.00 0.00 0.00 2.52
146 147 5.447010 CGAAGATGGCTGTTCTCTTCATTTC 60.447 44.000 10.95 0.00 43.19 2.17
147 148 4.394300 CGAAGATGGCTGTTCTCTTCATTT 59.606 41.667 10.95 0.00 43.19 2.32
148 149 3.937706 CGAAGATGGCTGTTCTCTTCATT 59.062 43.478 10.95 0.00 43.19 2.57
149 150 3.196469 TCGAAGATGGCTGTTCTCTTCAT 59.804 43.478 10.95 0.00 43.19 2.57
150 151 2.562738 TCGAAGATGGCTGTTCTCTTCA 59.437 45.455 10.95 0.00 43.19 3.02
151 152 3.238108 TCGAAGATGGCTGTTCTCTTC 57.762 47.619 0.00 0.00 40.84 2.87
152 153 3.902881 ATCGAAGATGGCTGTTCTCTT 57.097 42.857 0.00 0.00 45.12 2.85
153 154 3.320541 CCTATCGAAGATGGCTGTTCTCT 59.679 47.826 0.00 0.00 45.12 3.10
154 155 3.648009 CCTATCGAAGATGGCTGTTCTC 58.352 50.000 0.00 0.00 45.12 2.87
155 156 2.224161 GCCTATCGAAGATGGCTGTTCT 60.224 50.000 12.13 0.00 45.12 3.01
156 157 2.139118 GCCTATCGAAGATGGCTGTTC 58.861 52.381 12.13 0.00 45.12 3.18
157 158 2.246719 GCCTATCGAAGATGGCTGTT 57.753 50.000 12.13 0.00 45.12 3.16
158 159 3.997672 GCCTATCGAAGATGGCTGT 57.002 52.632 12.13 0.00 45.12 4.40
161 162 0.389166 CGGAGCCTATCGAAGATGGC 60.389 60.000 11.66 11.66 45.12 4.40
162 163 1.201181 CTCGGAGCCTATCGAAGATGG 59.799 57.143 0.00 0.00 45.12 3.51
163 164 1.201181 CCTCGGAGCCTATCGAAGATG 59.799 57.143 0.00 0.00 45.12 2.90
164 165 1.540267 CCTCGGAGCCTATCGAAGAT 58.460 55.000 0.00 0.00 45.12 2.40
165 166 0.537600 CCCTCGGAGCCTATCGAAGA 60.538 60.000 0.00 0.00 45.75 2.87
166 167 1.528292 CCCCTCGGAGCCTATCGAAG 61.528 65.000 0.00 0.00 34.87 3.79
167 168 1.530891 CCCCTCGGAGCCTATCGAA 60.531 63.158 0.00 0.00 34.87 3.71
168 169 2.115480 CCCCTCGGAGCCTATCGA 59.885 66.667 0.00 0.00 0.00 3.59
169 170 3.686045 GCCCCTCGGAGCCTATCG 61.686 72.222 0.00 0.00 0.00 2.92
170 171 2.524394 TGCCCCTCGGAGCCTATC 60.524 66.667 0.00 0.00 0.00 2.08
171 172 2.844839 GTGCCCCTCGGAGCCTAT 60.845 66.667 0.00 0.00 0.00 2.57
176 177 3.447025 GATTCGGTGCCCCTCGGAG 62.447 68.421 0.00 0.00 0.00 4.63
177 178 3.467226 GATTCGGTGCCCCTCGGA 61.467 66.667 0.00 0.00 0.00 4.55
178 179 3.447025 GAGATTCGGTGCCCCTCGG 62.447 68.421 0.00 0.00 0.00 4.63
179 180 1.961180 AAGAGATTCGGTGCCCCTCG 61.961 60.000 0.00 0.00 0.00 4.63
180 181 0.462759 CAAGAGATTCGGTGCCCCTC 60.463 60.000 0.00 0.00 0.00 4.30
181 182 1.201429 ACAAGAGATTCGGTGCCCCT 61.201 55.000 0.00 0.00 0.00 4.79
182 183 1.026718 CACAAGAGATTCGGTGCCCC 61.027 60.000 0.00 0.00 0.00 5.80
183 184 1.648467 GCACAAGAGATTCGGTGCCC 61.648 60.000 14.01 0.00 42.52 5.36
184 185 1.796796 GCACAAGAGATTCGGTGCC 59.203 57.895 14.01 0.00 42.52 5.01
185 186 0.674895 AGGCACAAGAGATTCGGTGC 60.675 55.000 15.66 15.66 45.30 5.01
186 187 2.166459 TCTAGGCACAAGAGATTCGGTG 59.834 50.000 0.00 0.00 32.36 4.94
187 188 2.166664 GTCTAGGCACAAGAGATTCGGT 59.833 50.000 0.00 0.00 0.00 4.69
188 189 2.166459 TGTCTAGGCACAAGAGATTCGG 59.834 50.000 0.00 0.00 0.00 4.30
189 190 3.510388 TGTCTAGGCACAAGAGATTCG 57.490 47.619 0.00 0.00 0.00 3.34
190 191 5.016051 TCATGTCTAGGCACAAGAGATTC 57.984 43.478 0.00 0.00 0.00 2.52
191 192 4.713814 TCTCATGTCTAGGCACAAGAGATT 59.286 41.667 17.29 0.00 43.06 2.40
192 193 4.285020 TCTCATGTCTAGGCACAAGAGAT 58.715 43.478 17.29 0.00 43.06 2.75
193 194 3.701664 TCTCATGTCTAGGCACAAGAGA 58.298 45.455 17.29 17.29 44.76 3.10
194 195 4.669206 ATCTCATGTCTAGGCACAAGAG 57.331 45.455 13.97 14.02 41.48 2.85
195 196 6.015603 CAGATATCTCATGTCTAGGCACAAGA 60.016 42.308 11.68 11.68 0.00 3.02
196 197 6.015603 TCAGATATCTCATGTCTAGGCACAAG 60.016 42.308 0.00 0.00 0.00 3.16
197 198 5.835280 TCAGATATCTCATGTCTAGGCACAA 59.165 40.000 0.00 0.00 0.00 3.33
198 199 5.388654 TCAGATATCTCATGTCTAGGCACA 58.611 41.667 0.00 0.00 0.00 4.57
199 200 5.973899 TCAGATATCTCATGTCTAGGCAC 57.026 43.478 0.00 0.00 0.00 5.01
200 201 6.983906 TTTCAGATATCTCATGTCTAGGCA 57.016 37.500 0.00 0.00 0.00 4.75
201 202 6.313411 GCATTTCAGATATCTCATGTCTAGGC 59.687 42.308 1.03 0.00 0.00 3.93
202 203 7.613585 AGCATTTCAGATATCTCATGTCTAGG 58.386 38.462 1.03 0.00 0.00 3.02
203 204 8.305317 TGAGCATTTCAGATATCTCATGTCTAG 58.695 37.037 1.03 0.00 0.00 2.43
204 205 8.186709 TGAGCATTTCAGATATCTCATGTCTA 57.813 34.615 1.03 0.00 0.00 2.59
205 206 7.063934 TGAGCATTTCAGATATCTCATGTCT 57.936 36.000 1.03 7.29 0.00 3.41
206 207 7.725818 TTGAGCATTTCAGATATCTCATGTC 57.274 36.000 1.03 6.88 37.07 3.06
207 208 7.308649 GCATTGAGCATTTCAGATATCTCATGT 60.309 37.037 1.03 0.00 44.79 3.21
208 209 7.024171 GCATTGAGCATTTCAGATATCTCATG 58.976 38.462 1.03 6.94 44.79 3.07
209 210 7.147143 GCATTGAGCATTTCAGATATCTCAT 57.853 36.000 1.03 0.00 44.79 2.90
210 211 6.555812 GCATTGAGCATTTCAGATATCTCA 57.444 37.500 1.03 0.00 44.79 3.27
225 226 2.932614 AGACTAATCGTGTGCATTGAGC 59.067 45.455 0.00 0.00 45.96 4.26
226 227 4.511457 CAGACTAATCGTGTGCATTGAG 57.489 45.455 0.00 0.00 29.53 3.02
233 234 3.419915 GCATTTGCAGACTAATCGTGTG 58.580 45.455 0.00 0.00 41.59 3.82
234 235 3.747099 GCATTTGCAGACTAATCGTGT 57.253 42.857 0.00 0.00 41.59 4.49
238 239 9.647652 TGGTGACAATGCATTTGCAGACTAATC 62.648 40.741 9.83 3.86 46.16 1.75
239 240 7.969773 TGGTGACAATGCATTTGCAGACTAAT 61.970 38.462 9.83 0.00 46.16 1.73
240 241 6.725895 TGGTGACAATGCATTTGCAGACTAA 61.726 40.000 9.83 0.00 46.16 2.24
241 242 5.286893 TGGTGACAATGCATTTGCAGACTA 61.287 41.667 9.83 0.00 46.16 2.59
242 243 4.561979 TGGTGACAATGCATTTGCAGACT 61.562 43.478 9.83 0.00 46.16 3.24
243 244 2.288334 TGGTGACAATGCATTTGCAGAC 60.288 45.455 9.83 7.42 46.16 3.51
244 245 1.962100 TGGTGACAATGCATTTGCAGA 59.038 42.857 9.83 0.00 46.16 4.26
245 246 2.442212 TGGTGACAATGCATTTGCAG 57.558 45.000 9.83 0.59 46.16 4.41
257 258 2.428890 GTGGTTTTGGTGATTGGTGACA 59.571 45.455 0.00 0.00 39.83 3.58
258 259 2.693074 AGTGGTTTTGGTGATTGGTGAC 59.307 45.455 0.00 0.00 0.00 3.67
259 260 3.025322 AGTGGTTTTGGTGATTGGTGA 57.975 42.857 0.00 0.00 0.00 4.02
260 261 3.817709 AAGTGGTTTTGGTGATTGGTG 57.182 42.857 0.00 0.00 0.00 4.17
261 262 3.895041 CCTAAGTGGTTTTGGTGATTGGT 59.105 43.478 0.00 0.00 0.00 3.67
262 263 3.258123 CCCTAAGTGGTTTTGGTGATTGG 59.742 47.826 0.00 0.00 30.68 3.16
263 264 4.148838 TCCCTAAGTGGTTTTGGTGATTG 58.851 43.478 0.00 0.00 30.68 2.67
264 265 4.105697 TCTCCCTAAGTGGTTTTGGTGATT 59.894 41.667 0.00 0.00 30.68 2.57
265 266 3.655777 TCTCCCTAAGTGGTTTTGGTGAT 59.344 43.478 0.00 0.00 30.68 3.06
266 267 3.050089 TCTCCCTAAGTGGTTTTGGTGA 58.950 45.455 0.00 0.00 30.68 4.02
267 268 3.502123 TCTCCCTAAGTGGTTTTGGTG 57.498 47.619 0.00 0.00 30.68 4.17
268 269 4.529716 TTTCTCCCTAAGTGGTTTTGGT 57.470 40.909 0.00 0.00 30.68 3.67
269 270 6.405842 GCATATTTCTCCCTAAGTGGTTTTGG 60.406 42.308 0.00 0.00 0.00 3.28
270 271 6.405842 GGCATATTTCTCCCTAAGTGGTTTTG 60.406 42.308 0.00 0.00 0.00 2.44
271 272 5.656859 GGCATATTTCTCCCTAAGTGGTTTT 59.343 40.000 0.00 0.00 0.00 2.43
272 273 5.201243 GGCATATTTCTCCCTAAGTGGTTT 58.799 41.667 0.00 0.00 0.00 3.27
273 274 4.386424 GGGCATATTTCTCCCTAAGTGGTT 60.386 45.833 0.00 0.00 37.08 3.67
274 275 3.138468 GGGCATATTTCTCCCTAAGTGGT 59.862 47.826 0.00 0.00 37.08 4.16
275 276 3.756117 GGGCATATTTCTCCCTAAGTGG 58.244 50.000 0.00 0.00 37.08 4.00
282 283 4.706842 TCTGTAAGGGCATATTTCTCCC 57.293 45.455 0.00 0.00 40.36 4.30
283 284 4.517075 GCTTCTGTAAGGGCATATTTCTCC 59.483 45.833 0.00 0.00 34.33 3.71
284 285 4.517075 GGCTTCTGTAAGGGCATATTTCTC 59.483 45.833 0.00 0.00 35.46 2.87
285 286 4.079787 TGGCTTCTGTAAGGGCATATTTCT 60.080 41.667 0.00 0.00 35.46 2.52
286 287 4.207165 TGGCTTCTGTAAGGGCATATTTC 58.793 43.478 0.00 0.00 35.46 2.17
287 288 4.249638 TGGCTTCTGTAAGGGCATATTT 57.750 40.909 0.00 0.00 35.46 1.40
288 289 3.951563 TGGCTTCTGTAAGGGCATATT 57.048 42.857 0.00 0.00 35.46 1.28
289 290 3.825328 CTTGGCTTCTGTAAGGGCATAT 58.175 45.455 0.00 0.00 35.46 1.78
290 291 2.683742 GCTTGGCTTCTGTAAGGGCATA 60.684 50.000 0.00 0.00 35.46 3.14
291 292 1.957113 GCTTGGCTTCTGTAAGGGCAT 60.957 52.381 0.00 0.00 35.46 4.40
292 293 0.609131 GCTTGGCTTCTGTAAGGGCA 60.609 55.000 0.00 0.00 35.46 5.36
293 294 0.609131 TGCTTGGCTTCTGTAAGGGC 60.609 55.000 0.00 0.00 32.98 5.19
294 295 1.168714 GTGCTTGGCTTCTGTAAGGG 58.831 55.000 0.00 0.00 32.98 3.95
295 296 1.896220 TGTGCTTGGCTTCTGTAAGG 58.104 50.000 0.00 0.00 32.98 2.69
296 297 4.036027 CCATATGTGCTTGGCTTCTGTAAG 59.964 45.833 1.24 0.00 35.68 2.34
297 298 3.947196 CCATATGTGCTTGGCTTCTGTAA 59.053 43.478 1.24 0.00 0.00 2.41
298 299 3.199727 TCCATATGTGCTTGGCTTCTGTA 59.800 43.478 1.24 0.00 32.80 2.74
299 300 2.025981 TCCATATGTGCTTGGCTTCTGT 60.026 45.455 1.24 0.00 32.80 3.41
300 301 2.646930 TCCATATGTGCTTGGCTTCTG 58.353 47.619 1.24 0.00 32.80 3.02
301 302 3.220110 CATCCATATGTGCTTGGCTTCT 58.780 45.455 1.24 0.00 32.80 2.85
386 387 6.377146 ACAAACTCTAGCAACCTTCTCAAAAA 59.623 34.615 0.00 0.00 0.00 1.94
419 420 6.350361 CCAAGCCATTGTAATTCAGAATGACA 60.350 38.462 9.10 9.10 39.67 3.58
431 432 0.963355 GGTCCGCCAAGCCATTGTAA 60.963 55.000 0.00 0.00 34.39 2.41
479 480 2.819422 TGTCGATAGTAGTCGTGCAC 57.181 50.000 6.82 6.82 42.07 4.57
526 527 5.723672 ATGAGTTGTTCTCCTTTCGACTA 57.276 39.130 0.00 0.00 42.12 2.59
528 529 4.865365 CCTATGAGTTGTTCTCCTTTCGAC 59.135 45.833 0.00 0.00 42.12 4.20
534 535 4.160329 TGTGTCCTATGAGTTGTTCTCCT 58.840 43.478 0.00 0.00 42.12 3.69
672 673 6.299805 AGTGTGCTTCTAATGAGTTATCCA 57.700 37.500 0.00 0.00 0.00 3.41
734 736 3.781079 TGCTGCGGAAATTTAAGGATG 57.219 42.857 0.00 0.00 0.00 3.51
914 946 4.710375 ACGGGAGATGTATATATGGTCCAC 59.290 45.833 0.00 0.00 0.00 4.02
1063 1096 7.634671 ATGATCACTTACAATTTGCATGAGA 57.365 32.000 0.00 0.00 0.00 3.27
1083 1116 5.448654 TGACTTGGCTGCCTTATAAATGAT 58.551 37.500 21.03 0.00 0.00 2.45
1228 1262 5.796350 AAATTGACGAAGGTGCAGTATAC 57.204 39.130 0.00 0.00 0.00 1.47
1240 1274 7.408132 TTGTTTTGTCACAAAAATTGACGAA 57.592 28.000 17.33 1.74 45.44 3.85
1493 1528 8.663911 CAAAGATTTTGCCTTAGTTTTGACAAA 58.336 29.630 0.00 0.00 0.00 2.83
1587 1625 5.388408 ACGAGAGTAGGATTTCGTTTTCT 57.612 39.130 0.00 0.00 46.88 2.52
1639 1677 3.483954 CAAGGATTGGATCACCGCT 57.516 52.632 0.00 0.00 43.94 5.52
1704 1742 2.444256 GCAGAGGCCGGGGTAATCT 61.444 63.158 2.18 0.00 0.00 2.40
2049 2096 4.470170 ATCGACACGCGCACGCTA 62.470 61.111 13.70 0.00 45.53 4.26


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

AutoCloner maintained by Alex Coulton.