Multiple sequence alignment - TraesCS1B01G289800

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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 TraesCS1B01G289800 chr1B 100.000 3762 0 0 1 3762 505608700 505612461 0.000000e+00 6948.0
1 TraesCS1B01G289800 chr1D 92.692 3585 195 34 205 3762 377948411 377951955 0.000000e+00 5107.0
2 TraesCS1B01G289800 chr1A 95.561 1532 49 9 2239 3762 478537319 478538839 0.000000e+00 2435.0
3 TraesCS1B01G289800 chr1A 94.441 1547 57 15 660 2191 478535469 478537001 0.000000e+00 2353.0
4 TraesCS1B01G289800 chr1A 87.541 305 30 5 308 606 478535168 478535470 2.780000e-91 346.0
5 TraesCS1B01G289800 chr3B 89.332 853 73 10 2279 3122 54286122 54286965 0.000000e+00 1055.0
6 TraesCS1B01G289800 chr3B 88.583 508 44 6 2624 3122 600749357 600748855 4.160000e-169 604.0
7 TraesCS1B01G289800 chr3B 87.402 508 50 7 2624 3122 600667813 600667311 4.220000e-159 571.0
8 TraesCS1B01G289800 chr3B 87.402 508 50 7 2624 3122 600702506 600702004 4.220000e-159 571.0
9 TraesCS1B01G289800 chr3B 94.545 165 8 1 2279 2443 600813348 600813185 1.730000e-63 254.0
10 TraesCS1B01G289800 chr3B 93.939 165 9 1 2279 2443 600726728 600726565 8.070000e-62 248.0
11 TraesCS1B01G289800 chr3B 91.875 160 12 1 2284 2443 600688487 600688329 4.890000e-54 222.0
12 TraesCS1B01G289800 chr3B 87.742 155 18 1 2438 2592 600667966 600667813 2.990000e-41 180.0
13 TraesCS1B01G289800 chr3B 85.806 155 20 2 2438 2592 600715640 600715488 3.010000e-36 163.0
14 TraesCS1B01G289800 chr3B 89.381 113 12 0 2480 2592 600749469 600749357 3.920000e-30 143.0
15 TraesCS1B01G289800 chr7B 88.277 853 82 11 2279 3122 81304534 81303691 0.000000e+00 1005.0
16 TraesCS1B01G289800 chr7B 95.610 205 8 1 1 204 578734527 578734731 1.010000e-85 327.0
17 TraesCS1B01G289800 chr7B 95.610 205 8 1 1 204 578755709 578755913 1.010000e-85 327.0
18 TraesCS1B01G289800 chr7B 73.973 292 48 24 274 551 145360565 145360842 4.000000e-15 93.5
19 TraesCS1B01G289800 chr2A 88.277 853 80 11 2279 3122 226114381 226115222 0.000000e+00 1003.0
20 TraesCS1B01G289800 chr3D 87.900 562 55 6 2568 3121 224776874 224777430 0.000000e+00 649.0
21 TraesCS1B01G289800 chr5B 95.610 205 8 1 1 204 378409488 378409692 1.010000e-85 327.0
22 TraesCS1B01G289800 chr5B 95.074 203 10 0 1 203 52843320 52843522 1.690000e-83 320.0
23 TraesCS1B01G289800 chr5B 94.146 205 11 1 1 204 334533277 334533481 1.010000e-80 311.0
24 TraesCS1B01G289800 chr2B 95.192 208 9 1 1 207 59296451 59296658 1.010000e-85 327.0
25 TraesCS1B01G289800 chr2B 94.634 205 11 0 1 205 421672987 421672783 6.060000e-83 318.0
26 TraesCS1B01G289800 chr6B 95.146 206 7 3 1 204 608865270 608865066 4.690000e-84 322.0
27 TraesCS1B01G289800 chr4B 94.146 205 11 1 1 204 614297039 614297243 1.010000e-80 311.0
28 TraesCS1B01G289800 chr7A 79.887 353 51 10 269 602 192372222 192371871 1.350000e-59 241.0
29 TraesCS1B01G289800 chr7A 88.235 51 6 0 205 255 735361082 735361032 1.130000e-05 62.1
30 TraesCS1B01G289800 chr7D 91.489 47 4 0 205 251 412685128 412685082 8.720000e-07 65.8
31 TraesCS1B01G289800 chr4D 100.000 34 0 0 212 245 88051838 88051871 3.140000e-06 63.9
32 TraesCS1B01G289800 chr5D 100.000 30 0 0 205 234 3503852 3503881 5.250000e-04 56.5


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 TraesCS1B01G289800 chr1B 505608700 505612461 3761 False 6948.000000 6948 100.000000 1 3762 1 chr1B.!!$F1 3761
1 TraesCS1B01G289800 chr1D 377948411 377951955 3544 False 5107.000000 5107 92.692000 205 3762 1 chr1D.!!$F1 3557
2 TraesCS1B01G289800 chr1A 478535168 478538839 3671 False 1711.333333 2435 92.514333 308 3762 3 chr1A.!!$F1 3454
3 TraesCS1B01G289800 chr3B 54286122 54286965 843 False 1055.000000 1055 89.332000 2279 3122 1 chr3B.!!$F1 843
4 TraesCS1B01G289800 chr3B 600702004 600702506 502 True 571.000000 571 87.402000 2624 3122 1 chr3B.!!$R2 498
5 TraesCS1B01G289800 chr3B 600667311 600667966 655 True 375.500000 571 87.572000 2438 3122 2 chr3B.!!$R6 684
6 TraesCS1B01G289800 chr3B 600748855 600749469 614 True 373.500000 604 88.982000 2480 3122 2 chr3B.!!$R7 642
7 TraesCS1B01G289800 chr7B 81303691 81304534 843 True 1005.000000 1005 88.277000 2279 3122 1 chr7B.!!$R1 843
8 TraesCS1B01G289800 chr2A 226114381 226115222 841 False 1003.000000 1003 88.277000 2279 3122 1 chr2A.!!$F1 843
9 TraesCS1B01G289800 chr3D 224776874 224777430 556 False 649.000000 649 87.900000 2568 3121 1 chr3D.!!$F1 553

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
118 119 0.103937 CGCCAAGGAGAGTCTCATCC 59.896 60.0 21.53 5.64 35.71 3.51 F
125 126 0.378962 GAGAGTCTCATCCGGACACG 59.621 60.0 15.53 0.00 36.29 4.49 F
1166 1186 0.107945 GCTCCAGTTTCCTCGATGCT 60.108 55.0 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1162 1.371558 GAGGAAACTGGAGCACCGT 59.628 57.895 0.0 0.0 44.43 4.83 R
2550 2870 0.037303 CACCAATGTCCTCCAGCACT 59.963 55.000 0.0 0.0 0.00 4.40 R
3142 3478 1.541233 GGAGGTCCACAGTTCACAGTG 60.541 57.143 0.0 0.0 35.64 3.66 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 3.899980 ACCCTCCGGTTTATATAGACACC 59.100 47.826 0.00 2.59 40.58 4.16
41 42 2.365105 CGGAGGGGGCTGGAGTTA 60.365 66.667 0.00 0.00 0.00 2.24
42 43 2.732619 CGGAGGGGGCTGGAGTTAC 61.733 68.421 0.00 0.00 0.00 2.50
43 44 1.615424 GGAGGGGGCTGGAGTTACA 60.615 63.158 0.00 0.00 0.00 2.41
44 45 1.602771 GAGGGGGCTGGAGTTACAC 59.397 63.158 0.00 0.00 0.00 2.90
45 46 1.151899 AGGGGGCTGGAGTTACACA 60.152 57.895 0.00 0.00 0.00 3.72
46 47 1.201429 AGGGGGCTGGAGTTACACAG 61.201 60.000 3.30 3.30 37.76 3.66
47 48 1.198759 GGGGGCTGGAGTTACACAGA 61.199 60.000 10.46 0.00 36.86 3.41
48 49 0.250513 GGGGCTGGAGTTACACAGAG 59.749 60.000 10.46 0.00 36.86 3.35
49 50 0.977395 GGGCTGGAGTTACACAGAGT 59.023 55.000 10.46 0.00 36.86 3.24
50 51 1.066787 GGGCTGGAGTTACACAGAGTC 60.067 57.143 10.46 0.00 36.86 3.36
51 52 1.402984 GGCTGGAGTTACACAGAGTCG 60.403 57.143 10.46 0.00 36.86 4.18
52 53 1.269998 GCTGGAGTTACACAGAGTCGT 59.730 52.381 10.46 0.00 36.86 4.34
53 54 2.288273 GCTGGAGTTACACAGAGTCGTT 60.288 50.000 10.46 0.00 36.86 3.85
54 55 3.799232 GCTGGAGTTACACAGAGTCGTTT 60.799 47.826 10.46 0.00 36.86 3.60
55 56 4.558095 GCTGGAGTTACACAGAGTCGTTTA 60.558 45.833 10.46 0.00 36.86 2.01
56 57 4.863491 TGGAGTTACACAGAGTCGTTTAC 58.137 43.478 0.00 0.00 0.00 2.01
57 58 4.338964 TGGAGTTACACAGAGTCGTTTACA 59.661 41.667 0.00 0.00 0.00 2.41
58 59 4.916249 GGAGTTACACAGAGTCGTTTACAG 59.084 45.833 0.00 0.00 0.00 2.74
59 60 5.278169 GGAGTTACACAGAGTCGTTTACAGA 60.278 44.000 0.00 0.00 0.00 3.41
60 61 5.759963 AGTTACACAGAGTCGTTTACAGAG 58.240 41.667 0.00 0.00 0.00 3.35
61 62 5.530171 AGTTACACAGAGTCGTTTACAGAGA 59.470 40.000 0.00 0.00 0.00 3.10
62 63 4.913335 ACACAGAGTCGTTTACAGAGAA 57.087 40.909 0.00 0.00 0.00 2.87
63 64 4.861210 ACACAGAGTCGTTTACAGAGAAG 58.139 43.478 0.00 0.00 0.00 2.85
64 65 4.230657 CACAGAGTCGTTTACAGAGAAGG 58.769 47.826 0.00 0.00 0.00 3.46
65 66 4.023107 CACAGAGTCGTTTACAGAGAAGGA 60.023 45.833 0.00 0.00 0.00 3.36
66 67 4.216687 ACAGAGTCGTTTACAGAGAAGGAG 59.783 45.833 0.00 0.00 0.00 3.69
67 68 4.456222 CAGAGTCGTTTACAGAGAAGGAGA 59.544 45.833 0.00 0.00 0.00 3.71
68 69 5.124776 CAGAGTCGTTTACAGAGAAGGAGAT 59.875 44.000 0.00 0.00 0.00 2.75
69 70 5.355910 AGAGTCGTTTACAGAGAAGGAGATC 59.644 44.000 0.00 0.00 0.00 2.75
70 71 5.258051 AGTCGTTTACAGAGAAGGAGATCT 58.742 41.667 0.00 0.00 0.00 2.75
71 72 6.416415 AGTCGTTTACAGAGAAGGAGATCTA 58.584 40.000 0.00 0.00 0.00 1.98
72 73 6.316890 AGTCGTTTACAGAGAAGGAGATCTAC 59.683 42.308 0.00 0.00 0.00 2.59
73 74 6.093771 GTCGTTTACAGAGAAGGAGATCTACA 59.906 42.308 7.93 0.00 0.00 2.74
74 75 6.829298 TCGTTTACAGAGAAGGAGATCTACAT 59.171 38.462 7.93 0.00 0.00 2.29
75 76 7.012515 TCGTTTACAGAGAAGGAGATCTACATC 59.987 40.741 7.93 4.66 0.00 3.06
76 77 7.201741 CGTTTACAGAGAAGGAGATCTACATCA 60.202 40.741 12.58 0.00 0.00 3.07
77 78 7.815840 TTACAGAGAAGGAGATCTACATCAG 57.184 40.000 12.58 4.68 0.00 2.90
78 79 6.012337 ACAGAGAAGGAGATCTACATCAGA 57.988 41.667 12.58 0.00 37.79 3.27
79 80 6.430864 ACAGAGAAGGAGATCTACATCAGAA 58.569 40.000 12.58 0.00 36.67 3.02
80 81 7.068702 ACAGAGAAGGAGATCTACATCAGAAT 58.931 38.462 12.58 0.00 36.67 2.40
81 82 7.231317 ACAGAGAAGGAGATCTACATCAGAATC 59.769 40.741 12.58 1.54 36.67 2.52
82 83 6.430925 AGAGAAGGAGATCTACATCAGAATCG 59.569 42.308 12.58 0.00 36.67 3.34
83 84 4.782019 AGGAGATCTACATCAGAATCGC 57.218 45.455 7.93 0.00 36.67 4.58
84 85 3.509575 AGGAGATCTACATCAGAATCGCC 59.490 47.826 7.93 0.00 36.67 5.54
85 86 3.256879 GGAGATCTACATCAGAATCGCCA 59.743 47.826 0.00 0.00 36.67 5.69
86 87 4.262207 GGAGATCTACATCAGAATCGCCAA 60.262 45.833 0.00 0.00 36.67 4.52
87 88 4.880759 AGATCTACATCAGAATCGCCAAG 58.119 43.478 0.00 0.00 36.67 3.61
88 89 2.826428 TCTACATCAGAATCGCCAAGC 58.174 47.619 0.00 0.00 0.00 4.01
89 90 2.432146 TCTACATCAGAATCGCCAAGCT 59.568 45.455 0.00 0.00 0.00 3.74
90 91 2.119801 ACATCAGAATCGCCAAGCTT 57.880 45.000 0.00 0.00 0.00 3.74
91 92 1.741706 ACATCAGAATCGCCAAGCTTG 59.258 47.619 19.93 19.93 0.00 4.01
92 93 0.737219 ATCAGAATCGCCAAGCTTGC 59.263 50.000 21.43 14.85 0.00 4.01
93 94 1.138247 CAGAATCGCCAAGCTTGCC 59.862 57.895 21.43 9.45 0.00 4.52
94 95 1.001641 AGAATCGCCAAGCTTGCCT 60.002 52.632 21.43 7.30 0.00 4.75
95 96 0.610232 AGAATCGCCAAGCTTGCCTT 60.610 50.000 21.43 10.35 0.00 4.35
96 97 0.179153 GAATCGCCAAGCTTGCCTTC 60.179 55.000 21.43 14.81 0.00 3.46
97 98 1.598701 AATCGCCAAGCTTGCCTTCC 61.599 55.000 21.43 5.26 0.00 3.46
98 99 2.769652 ATCGCCAAGCTTGCCTTCCA 62.770 55.000 21.43 1.33 0.00 3.53
99 100 2.653115 GCCAAGCTTGCCTTCCAC 59.347 61.111 21.43 0.12 0.00 4.02
100 101 2.956987 CCAAGCTTGCCTTCCACG 59.043 61.111 21.43 0.62 0.00 4.94
101 102 2.256461 CAAGCTTGCCTTCCACGC 59.744 61.111 14.65 0.00 38.87 5.34
102 103 2.985847 AAGCTTGCCTTCCACGCC 60.986 61.111 0.00 0.00 39.36 5.68
103 104 3.790416 AAGCTTGCCTTCCACGCCA 62.790 57.895 0.00 0.00 39.36 5.69
104 105 3.294493 GCTTGCCTTCCACGCCAA 61.294 61.111 0.00 0.00 32.93 4.52
105 106 2.956987 CTTGCCTTCCACGCCAAG 59.043 61.111 0.00 0.00 0.00 3.61
106 107 2.597217 TTGCCTTCCACGCCAAGG 60.597 61.111 3.73 3.73 43.13 3.61
107 108 3.126703 TTGCCTTCCACGCCAAGGA 62.127 57.895 10.97 0.00 42.94 3.36
108 109 2.747855 GCCTTCCACGCCAAGGAG 60.748 66.667 10.97 0.00 42.94 3.69
109 110 3.068881 CCTTCCACGCCAAGGAGA 58.931 61.111 2.12 0.00 42.94 3.71
110 111 1.078848 CCTTCCACGCCAAGGAGAG 60.079 63.158 2.12 0.00 42.94 3.20
111 112 1.674057 CTTCCACGCCAAGGAGAGT 59.326 57.895 0.00 0.00 36.33 3.24
112 113 0.390472 CTTCCACGCCAAGGAGAGTC 60.390 60.000 0.00 0.00 36.33 3.36
113 114 0.832135 TTCCACGCCAAGGAGAGTCT 60.832 55.000 0.00 0.00 36.33 3.24
114 115 1.216710 CCACGCCAAGGAGAGTCTC 59.783 63.158 12.01 12.01 0.00 3.36
115 116 1.536073 CCACGCCAAGGAGAGTCTCA 61.536 60.000 21.53 0.00 31.08 3.27
116 117 0.534412 CACGCCAAGGAGAGTCTCAT 59.466 55.000 21.53 12.32 31.08 2.90
117 118 0.820871 ACGCCAAGGAGAGTCTCATC 59.179 55.000 21.53 5.43 31.08 2.92
118 119 0.103937 CGCCAAGGAGAGTCTCATCC 59.896 60.000 21.53 5.64 35.71 3.51
119 120 0.103937 GCCAAGGAGAGTCTCATCCG 59.896 60.000 21.53 9.48 40.73 4.18
120 121 0.749649 CCAAGGAGAGTCTCATCCGG 59.250 60.000 21.53 14.39 40.73 5.14
121 122 1.686428 CCAAGGAGAGTCTCATCCGGA 60.686 57.143 21.53 6.61 40.73 5.14
122 123 1.407258 CAAGGAGAGTCTCATCCGGAC 59.593 57.143 21.53 0.00 40.73 4.79
123 124 0.626382 AGGAGAGTCTCATCCGGACA 59.374 55.000 21.53 0.00 40.73 4.02
124 125 0.741915 GGAGAGTCTCATCCGGACAC 59.258 60.000 21.53 0.74 36.29 3.67
125 126 0.378962 GAGAGTCTCATCCGGACACG 59.621 60.000 15.53 0.00 36.29 4.49
149 150 7.917720 GGAACGAAGTCTTCTATCTTGTATC 57.082 40.000 10.81 2.07 45.00 2.24
150 151 7.708998 GGAACGAAGTCTTCTATCTTGTATCT 58.291 38.462 10.81 0.00 45.00 1.98
151 152 8.192110 GGAACGAAGTCTTCTATCTTGTATCTT 58.808 37.037 10.81 0.00 45.00 2.40
152 153 9.228636 GAACGAAGTCTTCTATCTTGTATCTTC 57.771 37.037 10.81 0.00 45.00 2.87
153 154 8.282455 ACGAAGTCTTCTATCTTGTATCTTCA 57.718 34.615 10.81 0.00 29.74 3.02
154 155 8.908903 ACGAAGTCTTCTATCTTGTATCTTCAT 58.091 33.333 10.81 0.00 29.74 2.57
160 161 9.868160 TCTTCTATCTTGTATCTTCATAGTCCA 57.132 33.333 0.00 0.00 0.00 4.02
163 164 9.421399 TCTATCTTGTATCTTCATAGTCCAACA 57.579 33.333 0.00 0.00 0.00 3.33
164 165 9.689976 CTATCTTGTATCTTCATAGTCCAACAG 57.310 37.037 0.00 0.00 0.00 3.16
165 166 7.482169 TCTTGTATCTTCATAGTCCAACAGT 57.518 36.000 0.00 0.00 0.00 3.55
166 167 7.548097 TCTTGTATCTTCATAGTCCAACAGTC 58.452 38.462 0.00 0.00 0.00 3.51
167 168 6.222038 TGTATCTTCATAGTCCAACAGTCC 57.778 41.667 0.00 0.00 0.00 3.85
168 169 3.868757 TCTTCATAGTCCAACAGTCCG 57.131 47.619 0.00 0.00 0.00 4.79
169 170 2.496070 TCTTCATAGTCCAACAGTCCGG 59.504 50.000 0.00 0.00 0.00 5.14
170 171 0.535335 TCATAGTCCAACAGTCCGGC 59.465 55.000 0.00 0.00 0.00 6.13
171 172 0.537188 CATAGTCCAACAGTCCGGCT 59.463 55.000 0.00 0.00 0.00 5.52
185 186 3.557290 GGCTGTCCGGATACCCCC 61.557 72.222 7.81 0.00 0.00 5.40
186 187 2.446036 GCTGTCCGGATACCCCCT 60.446 66.667 7.81 0.00 0.00 4.79
187 188 2.070650 GCTGTCCGGATACCCCCTT 61.071 63.158 7.81 0.00 0.00 3.95
188 189 0.761702 GCTGTCCGGATACCCCCTTA 60.762 60.000 7.81 0.00 0.00 2.69
189 190 2.025636 CTGTCCGGATACCCCCTTAT 57.974 55.000 7.81 0.00 0.00 1.73
190 191 1.900486 CTGTCCGGATACCCCCTTATC 59.100 57.143 7.81 0.00 0.00 1.75
191 192 1.273759 GTCCGGATACCCCCTTATCC 58.726 60.000 7.81 0.00 43.00 2.59
192 193 0.868894 TCCGGATACCCCCTTATCCA 59.131 55.000 0.00 0.00 45.68 3.41
193 194 1.203262 TCCGGATACCCCCTTATCCAG 60.203 57.143 0.00 0.00 45.68 3.86
194 195 1.276622 CGGATACCCCCTTATCCAGG 58.723 60.000 9.33 0.00 45.68 4.45
252 253 1.524002 CTGTCGGCATGGAGGTGAT 59.476 57.895 0.00 0.00 0.00 3.06
256 257 2.592861 GGCATGGAGGTGATCGGC 60.593 66.667 0.00 0.00 0.00 5.54
261 262 1.899437 ATGGAGGTGATCGGCGTTGT 61.899 55.000 6.85 0.00 0.00 3.32
266 267 2.031919 TGATCGGCGTTGTTGGCT 59.968 55.556 6.85 0.00 0.00 4.75
267 268 1.017177 GTGATCGGCGTTGTTGGCTA 61.017 55.000 6.85 0.00 0.00 3.93
271 272 2.357760 GGCGTTGTTGGCTACGGA 60.358 61.111 0.00 0.00 42.42 4.69
277 278 2.180159 TTGTTGGCTACGGAGGAGGC 62.180 60.000 0.00 0.00 39.84 4.70
278 279 2.284331 TTGGCTACGGAGGAGGCA 60.284 61.111 4.29 4.29 46.73 4.75
309 310 2.745037 GTTGTGGGGGTGCTACGA 59.255 61.111 0.00 0.00 0.00 3.43
386 387 1.282653 TGTGGTGGGAGGTTTGTGGA 61.283 55.000 0.00 0.00 0.00 4.02
431 437 4.643387 ACTGGCAGGGGCGACAAC 62.643 66.667 20.34 0.00 42.47 3.32
443 449 4.278956 GACAACGTCGAGGGCATT 57.721 55.556 10.27 0.00 0.00 3.56
529 535 2.361230 GGGAAAGACAAGGGCGGG 60.361 66.667 0.00 0.00 0.00 6.13
559 565 1.666553 TTCGCGTCGATGCAAACCT 60.667 52.632 27.92 0.00 35.23 3.50
579 585 6.840780 ACCTGTCCCAAATTTAAATCTGAG 57.159 37.500 2.97 0.00 0.00 3.35
593 599 3.647649 CTGAGATGGGTCGCACGCA 62.648 63.158 8.11 8.11 45.21 5.24
644 650 3.273834 CGTTGGACCGCCGTTTGT 61.274 61.111 0.00 0.00 36.79 2.83
645 651 2.825975 CGTTGGACCGCCGTTTGTT 61.826 57.895 0.00 0.00 36.79 2.83
646 652 1.434287 GTTGGACCGCCGTTTGTTT 59.566 52.632 0.00 0.00 36.79 2.83
647 653 0.593008 GTTGGACCGCCGTTTGTTTC 60.593 55.000 0.00 0.00 36.79 2.78
648 654 1.030488 TTGGACCGCCGTTTGTTTCA 61.030 50.000 0.00 0.00 36.79 2.69
649 655 1.281656 GGACCGCCGTTTGTTTCAG 59.718 57.895 0.00 0.00 0.00 3.02
653 659 0.378962 CCGCCGTTTGTTTCAGTTCA 59.621 50.000 0.00 0.00 0.00 3.18
750 770 1.067821 CCACGCTCCTCTAATCCTCAC 59.932 57.143 0.00 0.00 0.00 3.51
752 772 0.676736 CGCTCCTCTAATCCTCACCC 59.323 60.000 0.00 0.00 0.00 4.61
753 773 1.052617 GCTCCTCTAATCCTCACCCC 58.947 60.000 0.00 0.00 0.00 4.95
754 774 1.723288 CTCCTCTAATCCTCACCCCC 58.277 60.000 0.00 0.00 0.00 5.40
755 775 1.221781 CTCCTCTAATCCTCACCCCCT 59.778 57.143 0.00 0.00 0.00 4.79
789 809 1.751924 CCAAACCGAGTCCACCAAAAA 59.248 47.619 0.00 0.00 0.00 1.94
894 914 3.129300 CGCGATCTGCCTTCCCTA 58.871 61.111 0.00 0.00 42.08 3.53
1152 1172 3.680786 CGAGTCCACGGTGCTCCA 61.681 66.667 5.52 0.00 0.00 3.86
1166 1186 0.107945 GCTCCAGTTTCCTCGATGCT 60.108 55.000 0.00 0.00 0.00 3.79
1223 1243 3.086282 TGTTAGGTGTCTGTATGCGAGA 58.914 45.455 0.00 0.00 0.00 4.04
1293 1313 9.905713 AATTTTTATGTTCTACTAGCATCCTCA 57.094 29.630 0.00 0.00 30.77 3.86
1297 1317 0.955178 TCTACTAGCATCCTCAGCGC 59.045 55.000 0.00 0.00 37.01 5.92
1299 1319 0.955178 TACTAGCATCCTCAGCGCTC 59.045 55.000 7.13 0.00 37.20 5.03
1469 1503 8.158132 TCAGTACAATTGTTAGTTATTGGTCCA 58.842 33.333 17.78 0.00 36.34 4.02
1471 1505 8.956426 AGTACAATTGTTAGTTATTGGTCCATG 58.044 33.333 17.78 0.00 36.34 3.66
1472 1506 8.952278 GTACAATTGTTAGTTATTGGTCCATGA 58.048 33.333 17.78 0.00 36.34 3.07
1474 1508 9.693739 ACAATTGTTAGTTATTGGTCCATGATA 57.306 29.630 4.92 0.00 36.34 2.15
1476 1510 9.920946 AATTGTTAGTTATTGGTCCATGATACT 57.079 29.630 0.00 0.00 0.00 2.12
1477 1511 8.731275 TTGTTAGTTATTGGTCCATGATACTG 57.269 34.615 0.00 0.00 0.00 2.74
1479 1513 8.544622 TGTTAGTTATTGGTCCATGATACTGAA 58.455 33.333 0.00 0.00 0.00 3.02
1480 1514 9.561069 GTTAGTTATTGGTCCATGATACTGAAT 57.439 33.333 0.00 0.00 0.00 2.57
1482 1516 8.682936 AGTTATTGGTCCATGATACTGAATTC 57.317 34.615 0.00 0.00 0.00 2.17
1483 1517 7.721399 AGTTATTGGTCCATGATACTGAATTCC 59.279 37.037 2.27 0.00 0.00 3.01
1484 1518 5.449297 TTGGTCCATGATACTGAATTCCA 57.551 39.130 2.27 0.00 0.00 3.53
1485 1519 5.651612 TGGTCCATGATACTGAATTCCAT 57.348 39.130 2.27 0.00 0.00 3.41
1486 1520 5.379187 TGGTCCATGATACTGAATTCCATG 58.621 41.667 12.23 12.23 35.61 3.66
1487 1521 5.132480 TGGTCCATGATACTGAATTCCATGA 59.868 40.000 17.94 6.50 37.41 3.07
1488 1522 6.183361 TGGTCCATGATACTGAATTCCATGAT 60.183 38.462 17.94 2.18 37.41 2.45
1489 1523 6.718454 GGTCCATGATACTGAATTCCATGATT 59.282 38.462 17.94 0.00 37.41 2.57
1490 1524 7.232127 GGTCCATGATACTGAATTCCATGATTT 59.768 37.037 17.94 0.00 37.41 2.17
1491 1525 8.636213 GTCCATGATACTGAATTCCATGATTTT 58.364 33.333 17.94 0.00 37.41 1.82
1591 1636 7.048512 GGCTAAACTGTAAGGTTCATGATACT 58.951 38.462 0.00 0.00 43.11 2.12
1806 1854 3.623060 TCTTATGGAATTTGCAGAGCGAC 59.377 43.478 0.00 0.00 0.00 5.19
1897 1945 6.000246 TGCACCCTATTAGAATGTTGATGA 58.000 37.500 0.00 0.00 0.00 2.92
1954 2002 6.788684 TTTCACCATTTCATCAGCAAAATG 57.211 33.333 0.00 0.00 40.78 2.32
1958 2006 5.697178 CACCATTTCATCAGCAAAATGAACA 59.303 36.000 8.89 0.00 42.71 3.18
1975 2023 4.431809 TGAACAAACTGCATTGAACCAAG 58.568 39.130 7.04 0.00 34.38 3.61
1986 2034 4.340381 GCATTGAACCAAGAGCATCCTTAT 59.660 41.667 0.00 0.00 33.66 1.73
2211 2259 1.836802 GCTCTCTCTCCCCTTCAATGT 59.163 52.381 0.00 0.00 0.00 2.71
2267 2585 8.478066 TGTACACTAGCTGAAATCATTGTATCT 58.522 33.333 0.00 0.00 0.00 1.98
2497 2817 2.094338 ACCACGATTACCGGACTTCTTC 60.094 50.000 9.46 0.00 43.93 2.87
2550 2870 5.011982 AGGATCCTTATATCCAGGTTCGA 57.988 43.478 9.02 0.00 46.81 3.71
2842 3169 7.504924 AGTTACTTAAACAGCAGCATAAACA 57.495 32.000 0.00 0.00 40.83 2.83
2917 3245 8.974060 ATGGTTACTGAACTCTTTTTCACTTA 57.026 30.769 0.00 0.00 35.74 2.24
2920 3248 8.671028 GGTTACTGAACTCTTTTTCACTTAACA 58.329 33.333 11.30 0.00 34.28 2.41
2936 3264 6.765989 TCACTTAACATGATATGGCTTGTACC 59.234 38.462 0.00 0.00 33.60 3.34
2953 3281 6.072119 GCTTGTACCATTAGCTACCAACTTTT 60.072 38.462 0.00 0.00 32.26 2.27
2973 3301 6.252655 ACTTTTAACTTGTGTCGTGCATTTTC 59.747 34.615 0.00 0.00 0.00 2.29
2980 3309 3.249799 TGTGTCGTGCATTTTCACCTTAG 59.750 43.478 0.00 0.00 33.57 2.18
3022 3352 5.355350 GTGAGCTGCAGATTTTAAGTACCAT 59.645 40.000 20.43 0.00 0.00 3.55
3089 3419 6.495181 ACTCTTGAGGTTCTGATTGAGACTTA 59.505 38.462 2.55 0.00 0.00 2.24
3090 3420 7.180051 ACTCTTGAGGTTCTGATTGAGACTTAT 59.820 37.037 2.55 0.00 0.00 1.73
3104 3434 9.133627 GATTGAGACTTATTGAAAAAGGAAAGC 57.866 33.333 0.00 0.00 0.00 3.51
3142 3478 2.639286 CACGAGGCAACACAAGGC 59.361 61.111 0.00 0.00 41.41 4.35
3247 3583 8.871686 ATGTTGTGACAGAATTTAAAACTTCC 57.128 30.769 0.00 0.00 39.58 3.46
3328 3664 8.682128 TGTTTTACTGAAAATGACAACTTGAC 57.318 30.769 0.00 0.00 36.92 3.18
3346 3682 5.130477 ACTTGACCTCAACCTGAAACTCTTA 59.870 40.000 0.00 0.00 0.00 2.10
3364 3700 7.736447 ACTCTTAATGTTTTCTGAGTTCTGG 57.264 36.000 0.00 0.00 31.71 3.86
3548 3884 4.397382 CAGTACATCTTTGTGCATCAACG 58.603 43.478 0.00 0.00 40.55 4.10
3560 3896 2.881513 TGCATCAACGTTCCTGCTTTAA 59.118 40.909 24.22 8.50 35.66 1.52
3595 3931 7.837202 TTATTTAAAGGTGTACTGGACATCG 57.163 36.000 0.00 0.00 44.64 3.84
3647 3983 3.567164 CACCACAAGTTTCTTGAGATGCT 59.433 43.478 15.04 0.00 0.00 3.79
3671 4007 5.365403 TTTATTCAGGGCAAACTTACACG 57.635 39.130 0.00 0.00 0.00 4.49
3702 4038 1.949525 GCAGTGTCATGTTGTTCCTGT 59.050 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.260128 CCCCTCCGGTGTCTATATAAACC 59.740 52.174 0.00 0.68 0.00 3.27
10 11 3.260128 CCCCCTCCGGTGTCTATATAAAC 59.740 52.174 0.00 0.00 0.00 2.01
11 12 3.513517 CCCCCTCCGGTGTCTATATAAA 58.486 50.000 0.00 0.00 0.00 1.40
12 13 2.824303 GCCCCCTCCGGTGTCTATATAA 60.824 54.545 0.00 0.00 0.00 0.98
13 14 1.272872 GCCCCCTCCGGTGTCTATATA 60.273 57.143 0.00 0.00 0.00 0.86
14 15 0.544595 GCCCCCTCCGGTGTCTATAT 60.545 60.000 0.00 0.00 0.00 0.86
15 16 1.152398 GCCCCCTCCGGTGTCTATA 60.152 63.158 0.00 0.00 0.00 1.31
16 17 2.446036 GCCCCCTCCGGTGTCTAT 60.446 66.667 0.00 0.00 0.00 1.98
17 18 3.680196 AGCCCCCTCCGGTGTCTA 61.680 66.667 0.00 0.00 0.00 2.59
23 24 3.995809 TAACTCCAGCCCCCTCCGG 62.996 68.421 0.00 0.00 0.00 5.14
24 25 2.365105 TAACTCCAGCCCCCTCCG 60.365 66.667 0.00 0.00 0.00 4.63
25 26 1.615424 TGTAACTCCAGCCCCCTCC 60.615 63.158 0.00 0.00 0.00 4.30
26 27 1.198759 TGTGTAACTCCAGCCCCCTC 61.199 60.000 0.00 0.00 38.04 4.30
27 28 1.151899 TGTGTAACTCCAGCCCCCT 60.152 57.895 0.00 0.00 38.04 4.79
28 29 1.198759 TCTGTGTAACTCCAGCCCCC 61.199 60.000 0.00 0.00 38.04 5.40
29 30 0.250513 CTCTGTGTAACTCCAGCCCC 59.749 60.000 0.00 0.00 38.04 5.80
30 31 0.977395 ACTCTGTGTAACTCCAGCCC 59.023 55.000 0.00 0.00 38.04 5.19
31 32 1.402984 CGACTCTGTGTAACTCCAGCC 60.403 57.143 0.00 0.00 38.04 4.85
32 33 1.269998 ACGACTCTGTGTAACTCCAGC 59.730 52.381 0.00 0.00 38.04 4.85
33 34 3.644884 AACGACTCTGTGTAACTCCAG 57.355 47.619 0.00 0.00 38.04 3.86
34 35 4.338964 TGTAAACGACTCTGTGTAACTCCA 59.661 41.667 0.00 0.00 38.04 3.86
35 36 4.863491 TGTAAACGACTCTGTGTAACTCC 58.137 43.478 0.00 0.00 38.04 3.85
36 37 5.755813 TCTGTAAACGACTCTGTGTAACTC 58.244 41.667 0.00 0.00 38.04 3.01
37 38 5.530171 TCTCTGTAAACGACTCTGTGTAACT 59.470 40.000 0.00 0.00 38.04 2.24
38 39 5.755813 TCTCTGTAAACGACTCTGTGTAAC 58.244 41.667 0.00 0.00 37.35 2.50
39 40 6.381481 TTCTCTGTAAACGACTCTGTGTAA 57.619 37.500 0.00 0.00 0.00 2.41
40 41 5.048921 CCTTCTCTGTAAACGACTCTGTGTA 60.049 44.000 0.00 0.00 0.00 2.90
41 42 4.261656 CCTTCTCTGTAAACGACTCTGTGT 60.262 45.833 0.00 0.00 0.00 3.72
42 43 4.023107 TCCTTCTCTGTAAACGACTCTGTG 60.023 45.833 0.00 0.00 0.00 3.66
43 44 4.142790 TCCTTCTCTGTAAACGACTCTGT 58.857 43.478 0.00 0.00 0.00 3.41
44 45 4.456222 TCTCCTTCTCTGTAAACGACTCTG 59.544 45.833 0.00 0.00 0.00 3.35
45 46 4.653868 TCTCCTTCTCTGTAAACGACTCT 58.346 43.478 0.00 0.00 0.00 3.24
46 47 5.355910 AGATCTCCTTCTCTGTAAACGACTC 59.644 44.000 0.00 0.00 0.00 3.36
47 48 5.258051 AGATCTCCTTCTCTGTAAACGACT 58.742 41.667 0.00 0.00 0.00 4.18
48 49 5.570234 AGATCTCCTTCTCTGTAAACGAC 57.430 43.478 0.00 0.00 0.00 4.34
49 50 6.178324 TGTAGATCTCCTTCTCTGTAAACGA 58.822 40.000 0.00 0.00 0.00 3.85
50 51 6.438259 TGTAGATCTCCTTCTCTGTAAACG 57.562 41.667 0.00 0.00 0.00 3.60
51 52 8.001881 TGATGTAGATCTCCTTCTCTGTAAAC 57.998 38.462 0.00 0.00 0.00 2.01
52 53 8.055790 TCTGATGTAGATCTCCTTCTCTGTAAA 58.944 37.037 0.00 0.00 0.00 2.01
53 54 7.578203 TCTGATGTAGATCTCCTTCTCTGTAA 58.422 38.462 0.00 0.00 0.00 2.41
54 55 7.142995 TCTGATGTAGATCTCCTTCTCTGTA 57.857 40.000 0.00 0.00 0.00 2.74
55 56 6.012337 TCTGATGTAGATCTCCTTCTCTGT 57.988 41.667 0.00 0.00 0.00 3.41
56 57 6.957920 TTCTGATGTAGATCTCCTTCTCTG 57.042 41.667 0.00 0.00 34.80 3.35
57 58 6.430925 CGATTCTGATGTAGATCTCCTTCTCT 59.569 42.308 0.00 0.00 34.80 3.10
58 59 6.611381 CGATTCTGATGTAGATCTCCTTCTC 58.389 44.000 0.00 0.00 34.80 2.87
59 60 5.048083 GCGATTCTGATGTAGATCTCCTTCT 60.048 44.000 0.00 0.00 34.80 2.85
60 61 5.160641 GCGATTCTGATGTAGATCTCCTTC 58.839 45.833 0.00 0.00 34.80 3.46
61 62 4.021544 GGCGATTCTGATGTAGATCTCCTT 60.022 45.833 0.00 0.00 34.80 3.36
62 63 3.509575 GGCGATTCTGATGTAGATCTCCT 59.490 47.826 0.00 0.00 34.80 3.69
63 64 3.256879 TGGCGATTCTGATGTAGATCTCC 59.743 47.826 0.00 0.00 34.80 3.71
64 65 4.511617 TGGCGATTCTGATGTAGATCTC 57.488 45.455 0.00 0.00 34.80 2.75
65 66 4.798924 GCTTGGCGATTCTGATGTAGATCT 60.799 45.833 0.00 0.00 34.80 2.75
66 67 3.431572 GCTTGGCGATTCTGATGTAGATC 59.568 47.826 0.00 0.00 34.80 2.75
67 68 3.070734 AGCTTGGCGATTCTGATGTAGAT 59.929 43.478 0.00 0.00 34.80 1.98
68 69 2.432146 AGCTTGGCGATTCTGATGTAGA 59.568 45.455 0.00 0.00 0.00 2.59
69 70 2.831333 AGCTTGGCGATTCTGATGTAG 58.169 47.619 0.00 0.00 0.00 2.74
70 71 2.938451 CAAGCTTGGCGATTCTGATGTA 59.062 45.455 19.14 0.00 0.00 2.29
71 72 1.741706 CAAGCTTGGCGATTCTGATGT 59.258 47.619 19.14 0.00 0.00 3.06
72 73 1.533338 GCAAGCTTGGCGATTCTGATG 60.533 52.381 27.10 0.00 0.00 3.07
73 74 0.737219 GCAAGCTTGGCGATTCTGAT 59.263 50.000 27.10 0.00 0.00 2.90
74 75 1.308069 GGCAAGCTTGGCGATTCTGA 61.308 55.000 33.68 0.00 43.97 3.27
75 76 1.138247 GGCAAGCTTGGCGATTCTG 59.862 57.895 33.68 4.48 43.97 3.02
76 77 3.595819 GGCAAGCTTGGCGATTCT 58.404 55.556 33.68 0.00 43.97 2.40
83 84 2.956987 CGTGGAAGGCAAGCTTGG 59.043 61.111 27.10 9.80 0.00 3.61
92 93 1.078848 CTCTCCTTGGCGTGGAAGG 60.079 63.158 0.00 0.00 41.36 3.46
93 94 0.390472 GACTCTCCTTGGCGTGGAAG 60.390 60.000 0.17 3.93 32.61 3.46
94 95 0.832135 AGACTCTCCTTGGCGTGGAA 60.832 55.000 0.17 0.00 32.61 3.53
95 96 1.228894 AGACTCTCCTTGGCGTGGA 60.229 57.895 0.00 0.00 0.00 4.02
96 97 1.216710 GAGACTCTCCTTGGCGTGG 59.783 63.158 0.00 0.00 0.00 4.94
97 98 0.534412 ATGAGACTCTCCTTGGCGTG 59.466 55.000 3.68 0.00 0.00 5.34
98 99 0.820871 GATGAGACTCTCCTTGGCGT 59.179 55.000 3.68 0.00 0.00 5.68
99 100 0.103937 GGATGAGACTCTCCTTGGCG 59.896 60.000 3.68 0.00 0.00 5.69
100 101 0.103937 CGGATGAGACTCTCCTTGGC 59.896 60.000 14.97 0.00 0.00 4.52
101 102 0.749649 CCGGATGAGACTCTCCTTGG 59.250 60.000 0.00 8.77 0.00 3.61
102 103 1.407258 GTCCGGATGAGACTCTCCTTG 59.593 57.143 7.81 8.87 0.00 3.61
103 104 1.006043 TGTCCGGATGAGACTCTCCTT 59.994 52.381 7.81 0.00 35.21 3.36
104 105 0.626382 TGTCCGGATGAGACTCTCCT 59.374 55.000 7.81 0.00 35.21 3.69
105 106 0.741915 GTGTCCGGATGAGACTCTCC 59.258 60.000 7.81 7.35 34.50 3.71
106 107 0.378962 CGTGTCCGGATGAGACTCTC 59.621 60.000 7.81 0.00 35.16 3.20
107 108 2.483441 CGTGTCCGGATGAGACTCT 58.517 57.895 7.81 0.00 35.16 3.24
118 119 0.318445 AAGACTTCGTTCCGTGTCCG 60.318 55.000 0.00 0.00 34.39 4.79
119 120 1.000496 AGAAGACTTCGTTCCGTGTCC 60.000 52.381 9.53 0.00 34.39 4.02
120 121 2.418983 AGAAGACTTCGTTCCGTGTC 57.581 50.000 9.53 0.00 34.21 3.67
121 122 3.757493 AGATAGAAGACTTCGTTCCGTGT 59.243 43.478 9.53 0.00 34.02 4.49
122 123 4.358494 AGATAGAAGACTTCGTTCCGTG 57.642 45.455 9.53 0.00 34.02 4.94
123 124 4.217983 ACAAGATAGAAGACTTCGTTCCGT 59.782 41.667 9.53 7.97 34.02 4.69
124 125 4.734917 ACAAGATAGAAGACTTCGTTCCG 58.265 43.478 9.53 7.45 34.02 4.30
125 126 7.708998 AGATACAAGATAGAAGACTTCGTTCC 58.291 38.462 9.53 1.49 34.02 3.62
126 127 9.228636 GAAGATACAAGATAGAAGACTTCGTTC 57.771 37.037 9.53 10.20 34.02 3.95
127 128 8.740906 TGAAGATACAAGATAGAAGACTTCGTT 58.259 33.333 9.53 1.33 35.49 3.85
128 129 8.282455 TGAAGATACAAGATAGAAGACTTCGT 57.718 34.615 9.53 2.90 35.49 3.85
134 135 9.868160 TGGACTATGAAGATACAAGATAGAAGA 57.132 33.333 0.00 0.00 0.00 2.87
137 138 9.421399 TGTTGGACTATGAAGATACAAGATAGA 57.579 33.333 0.00 0.00 0.00 1.98
138 139 9.689976 CTGTTGGACTATGAAGATACAAGATAG 57.310 37.037 0.00 0.00 0.00 2.08
139 140 9.201989 ACTGTTGGACTATGAAGATACAAGATA 57.798 33.333 0.00 0.00 0.00 1.98
140 141 8.083828 ACTGTTGGACTATGAAGATACAAGAT 57.916 34.615 0.00 0.00 0.00 2.40
141 142 7.363880 GGACTGTTGGACTATGAAGATACAAGA 60.364 40.741 0.00 0.00 0.00 3.02
142 143 6.758886 GGACTGTTGGACTATGAAGATACAAG 59.241 42.308 0.00 0.00 0.00 3.16
143 144 6.627287 CGGACTGTTGGACTATGAAGATACAA 60.627 42.308 0.00 0.00 0.00 2.41
144 145 5.163550 CGGACTGTTGGACTATGAAGATACA 60.164 44.000 0.00 0.00 0.00 2.29
145 146 5.282510 CGGACTGTTGGACTATGAAGATAC 58.717 45.833 0.00 0.00 0.00 2.24
146 147 4.341235 CCGGACTGTTGGACTATGAAGATA 59.659 45.833 0.00 0.00 0.00 1.98
147 148 3.133003 CCGGACTGTTGGACTATGAAGAT 59.867 47.826 0.00 0.00 0.00 2.40
148 149 2.496070 CCGGACTGTTGGACTATGAAGA 59.504 50.000 0.00 0.00 0.00 2.87
149 150 2.893637 CCGGACTGTTGGACTATGAAG 58.106 52.381 0.00 0.00 0.00 3.02
150 151 1.066430 GCCGGACTGTTGGACTATGAA 60.066 52.381 5.05 0.00 0.00 2.57
151 152 0.535335 GCCGGACTGTTGGACTATGA 59.465 55.000 5.05 0.00 0.00 2.15
152 153 0.537188 AGCCGGACTGTTGGACTATG 59.463 55.000 5.05 0.00 0.00 2.23
153 154 0.537188 CAGCCGGACTGTTGGACTAT 59.463 55.000 5.05 0.00 41.86 2.12
154 155 1.972198 CAGCCGGACTGTTGGACTA 59.028 57.895 5.05 0.00 41.86 2.59
155 156 2.743718 CAGCCGGACTGTTGGACT 59.256 61.111 5.05 0.00 41.86 3.85
168 169 3.557290 GGGGGTATCCGGACAGCC 61.557 72.222 23.00 23.00 36.01 4.85
169 170 0.761702 TAAGGGGGTATCCGGACAGC 60.762 60.000 6.12 4.13 36.01 4.40
170 171 1.900486 GATAAGGGGGTATCCGGACAG 59.100 57.143 6.12 0.00 36.01 3.51
171 172 1.483686 GGATAAGGGGGTATCCGGACA 60.484 57.143 6.12 0.00 40.10 4.02
172 173 1.273759 GGATAAGGGGGTATCCGGAC 58.726 60.000 6.12 0.00 40.10 4.79
173 174 3.801034 GGATAAGGGGGTATCCGGA 57.199 57.895 6.61 6.61 40.10 5.14
185 186 2.043227 GGTGAGGGAGTCCTGGATAAG 58.957 57.143 9.58 0.00 45.05 1.73
186 187 1.344087 GGGTGAGGGAGTCCTGGATAA 60.344 57.143 9.58 0.00 45.05 1.75
187 188 0.264955 GGGTGAGGGAGTCCTGGATA 59.735 60.000 9.58 0.00 45.05 2.59
188 189 1.003573 GGGTGAGGGAGTCCTGGAT 59.996 63.158 9.58 0.00 45.05 3.41
189 190 2.450243 GGGTGAGGGAGTCCTGGA 59.550 66.667 9.58 0.00 45.05 3.86
190 191 3.077556 CGGGTGAGGGAGTCCTGG 61.078 72.222 9.58 0.00 45.05 4.45
191 192 3.775654 GCGGGTGAGGGAGTCCTG 61.776 72.222 9.58 0.00 45.05 3.86
194 195 4.131088 GACGCGGGTGAGGGAGTC 62.131 72.222 10.96 0.00 0.00 3.36
195 196 4.680537 AGACGCGGGTGAGGGAGT 62.681 66.667 10.96 0.00 0.00 3.85
196 197 3.827898 GAGACGCGGGTGAGGGAG 61.828 72.222 10.96 0.00 0.00 4.30
197 198 4.361971 AGAGACGCGGGTGAGGGA 62.362 66.667 10.96 0.00 0.00 4.20
198 199 3.827898 GAGAGACGCGGGTGAGGG 61.828 72.222 10.96 0.00 0.00 4.30
199 200 3.827898 GGAGAGACGCGGGTGAGG 61.828 72.222 10.96 0.00 0.00 3.86
200 201 3.827898 GGGAGAGACGCGGGTGAG 61.828 72.222 10.96 0.00 0.00 3.51
201 202 4.671590 TGGGAGAGACGCGGGTGA 62.672 66.667 10.96 0.00 0.00 4.02
202 203 4.135153 CTGGGAGAGACGCGGGTG 62.135 72.222 10.96 0.00 34.71 4.61
203 204 4.361971 TCTGGGAGAGACGCGGGT 62.362 66.667 12.47 4.12 38.20 5.28
234 235 0.531532 GATCACCTCCATGCCGACAG 60.532 60.000 0.00 0.00 0.00 3.51
252 253 2.735478 CGTAGCCAACAACGCCGA 60.735 61.111 0.00 0.00 31.66 5.54
256 257 0.736325 CTCCTCCGTAGCCAACAACG 60.736 60.000 0.00 0.00 38.80 4.10
261 262 1.899437 CTTGCCTCCTCCGTAGCCAA 61.899 60.000 0.00 0.00 0.00 4.52
266 267 2.365105 CCCCTTGCCTCCTCCGTA 60.365 66.667 0.00 0.00 0.00 4.02
277 278 4.596585 AACCACGCCACCCCCTTG 62.597 66.667 0.00 0.00 0.00 3.61
278 279 4.596585 CAACCACGCCACCCCCTT 62.597 66.667 0.00 0.00 0.00 3.95
288 289 3.185299 TAGCACCCCCACAACCACG 62.185 63.158 0.00 0.00 0.00 4.94
309 310 3.343421 GACTGTTTTCGCCGCCGT 61.343 61.111 0.00 0.00 35.54 5.68
369 370 0.112218 CATCCACAAACCTCCCACCA 59.888 55.000 0.00 0.00 0.00 4.17
431 437 3.499737 GCCACAATGCCCTCGACG 61.500 66.667 0.00 0.00 0.00 5.12
441 447 0.540365 CCAACACTCCTGGCCACAAT 60.540 55.000 0.00 0.00 0.00 2.71
443 449 1.932156 AACCAACACTCCTGGCCACA 61.932 55.000 0.00 0.00 37.48 4.17
450 456 3.650942 TCCTATCAACAACCAACACTCCT 59.349 43.478 0.00 0.00 0.00 3.69
539 545 3.631451 TTTGCATCGACGCGAACA 58.369 50.000 15.93 0.00 39.99 3.18
542 548 2.048597 AGGTTTGCATCGACGCGA 60.049 55.556 15.93 0.00 41.13 5.87
559 565 6.380846 CCCATCTCAGATTTAAATTTGGGACA 59.619 38.462 20.29 3.46 43.21 4.02
579 585 3.188786 GTCTGCGTGCGACCCATC 61.189 66.667 0.00 0.00 0.00 3.51
614 620 0.376152 TCCAACGCGTCGAGATAGAC 59.624 55.000 14.44 0.00 37.76 2.59
641 647 6.202188 GTCCGTTTAGATCTGAACTGAAACAA 59.798 38.462 23.35 6.65 27.89 2.83
642 648 5.694910 GTCCGTTTAGATCTGAACTGAAACA 59.305 40.000 23.35 3.57 27.89 2.83
643 649 5.164080 CGTCCGTTTAGATCTGAACTGAAAC 60.164 44.000 23.35 14.97 27.89 2.78
644 650 4.921515 CGTCCGTTTAGATCTGAACTGAAA 59.078 41.667 23.35 5.55 27.89 2.69
645 651 4.482386 CGTCCGTTTAGATCTGAACTGAA 58.518 43.478 23.35 9.53 27.89 3.02
646 652 3.119602 CCGTCCGTTTAGATCTGAACTGA 60.120 47.826 23.35 20.16 0.00 3.41
647 653 3.179830 CCGTCCGTTTAGATCTGAACTG 58.820 50.000 23.35 18.50 0.00 3.16
648 654 2.416972 GCCGTCCGTTTAGATCTGAACT 60.417 50.000 23.35 0.00 0.00 3.01
649 655 1.925185 GCCGTCCGTTTAGATCTGAAC 59.075 52.381 18.03 18.03 0.00 3.18
653 659 1.226888 GCGCCGTCCGTTTAGATCT 60.227 57.895 0.00 0.00 39.71 2.75
906 926 2.507944 GATCTGCCACGGCTGGAT 59.492 61.111 14.15 14.02 40.55 3.41
985 1005 2.621672 TACATCCTGCCCCTCCTCCC 62.622 65.000 0.00 0.00 0.00 4.30
1142 1162 1.371558 GAGGAAACTGGAGCACCGT 59.628 57.895 0.00 0.00 44.43 4.83
1166 1186 4.745172 GCAAAATTGGGCCCTAAAACAGAA 60.745 41.667 25.70 6.32 0.00 3.02
1474 1508 7.043565 GCCATAACAAAATCATGGAATTCAGT 58.956 34.615 7.93 0.00 41.53 3.41
1476 1510 6.944096 TGCCATAACAAAATCATGGAATTCA 58.056 32.000 7.93 0.00 41.53 2.57
1477 1511 7.333921 TGTTGCCATAACAAAATCATGGAATTC 59.666 33.333 4.04 0.00 41.53 2.17
1479 1513 6.709281 TGTTGCCATAACAAAATCATGGAAT 58.291 32.000 4.04 0.00 41.53 3.01
1480 1514 6.106648 TGTTGCCATAACAAAATCATGGAA 57.893 33.333 4.04 0.00 41.53 3.53
1481 1515 5.735285 TGTTGCCATAACAAAATCATGGA 57.265 34.783 4.04 0.00 41.53 3.41
1482 1516 6.256975 CAGATGTTGCCATAACAAAATCATGG 59.743 38.462 9.45 0.00 43.81 3.66
1483 1517 6.814644 ACAGATGTTGCCATAACAAAATCATG 59.185 34.615 9.45 7.40 43.81 3.07
1484 1518 6.938507 ACAGATGTTGCCATAACAAAATCAT 58.061 32.000 9.45 0.00 43.81 2.45
1485 1519 6.343716 ACAGATGTTGCCATAACAAAATCA 57.656 33.333 9.45 0.00 43.81 2.57
1486 1520 7.656707 AAACAGATGTTGCCATAACAAAATC 57.343 32.000 0.00 0.11 42.36 2.17
1487 1521 8.367156 AGTAAACAGATGTTGCCATAACAAAAT 58.633 29.630 0.00 0.00 38.44 1.82
1488 1522 7.721402 AGTAAACAGATGTTGCCATAACAAAA 58.279 30.769 0.00 0.00 38.44 2.44
1489 1523 7.230510 AGAGTAAACAGATGTTGCCATAACAAA 59.769 33.333 0.00 0.00 38.44 2.83
1490 1524 6.714810 AGAGTAAACAGATGTTGCCATAACAA 59.285 34.615 0.00 0.00 38.44 2.83
1491 1525 6.149308 CAGAGTAAACAGATGTTGCCATAACA 59.851 38.462 0.00 0.00 38.44 2.41
1527 1572 2.375174 ACAATTACAGGGAAGAGTGGCA 59.625 45.455 0.00 0.00 0.00 4.92
1591 1636 8.970020 ACTTTAACAGCAATATCATGGAATTCA 58.030 29.630 7.93 0.00 0.00 2.57
1806 1854 7.380870 CACTCTCTAATGACCTGATCAAATACG 59.619 40.741 0.00 0.00 41.93 3.06
1897 1945 5.141182 ACTCACAGGTCGAGGTTATATGAT 58.859 41.667 0.00 0.00 34.66 2.45
1954 2002 4.681744 TCTTGGTTCAATGCAGTTTGTTC 58.318 39.130 0.00 0.00 0.00 3.18
1958 2006 2.694628 TGCTCTTGGTTCAATGCAGTTT 59.305 40.909 0.00 0.00 32.38 2.66
1986 2034 5.316167 ACACTTTGATGTGAGGATAGCAAA 58.684 37.500 1.47 0.00 40.12 3.68
2211 2259 7.880160 AAGCAGGTTAAGCATGTATAATCAA 57.120 32.000 7.52 0.00 0.00 2.57
2267 2585 3.689347 TCTGCTCGGTTGTACCTAGTTA 58.311 45.455 0.00 0.00 33.90 2.24
2358 2677 6.092748 GCTTCTGAAGTACTCTTTCTCTGAG 58.907 44.000 17.97 0.00 37.55 3.35
2550 2870 0.037303 CACCAATGTCCTCCAGCACT 59.963 55.000 0.00 0.00 0.00 4.40
2646 2966 8.438676 ACAGATAGCAAACCTGTGATATAAAC 57.561 34.615 0.00 0.00 39.43 2.01
2842 3169 3.084039 CCAGCACTGGTCAATGTATTGT 58.916 45.455 8.61 0.00 45.53 2.71
2936 3264 8.349983 ACACAAGTTAAAAGTTGGTAGCTAATG 58.650 33.333 13.37 4.28 42.30 1.90
2953 3281 4.496673 GGTGAAAATGCACGACACAAGTTA 60.497 41.667 14.01 0.00 39.66 2.24
2973 3301 8.137437 ACAGACATTGATTCAAAAACTAAGGTG 58.863 33.333 2.68 0.00 0.00 4.00
2980 3309 6.143438 CAGCTCACAGACATTGATTCAAAAAC 59.857 38.462 2.68 0.00 0.00 2.43
3022 3352 2.287547 GCAGCGAAGAAAATGTTGTGGA 60.288 45.455 0.00 0.00 0.00 4.02
3104 3434 4.689812 GTGCCTCTGAAGATAGCATATGTG 59.310 45.833 4.29 0.00 36.21 3.21
3142 3478 1.541233 GGAGGTCCACAGTTCACAGTG 60.541 57.143 0.00 0.00 35.64 3.66
3328 3664 6.884280 AACATTAAGAGTTTCAGGTTGAGG 57.116 37.500 0.00 0.00 0.00 3.86
3346 3682 5.127682 AGTTTGCCAGAACTCAGAAAACATT 59.872 36.000 0.00 0.00 34.94 2.71
3364 3700 2.550180 GGGAGAGAACAGTTGAGTTTGC 59.450 50.000 0.00 0.00 0.00 3.68
3437 3773 4.523083 AGTTGTTGCCTCTGACTAAACAA 58.477 39.130 0.00 0.00 38.15 2.83
3595 3931 3.258971 AGATGCCAGTCTCAACTAAGC 57.741 47.619 0.00 0.00 35.52 3.09
3647 3983 6.210078 CGTGTAAGTTTGCCCTGAATAAAAA 58.790 36.000 0.00 0.00 0.00 1.94
3671 4007 0.321034 TGACACTGCACTCATCCAGC 60.321 55.000 0.00 0.00 32.37 4.85
3702 4038 6.376864 CCAACATGTGTAACCAGGAATTATGA 59.623 38.462 0.00 0.00 34.36 2.15


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

AutoCloner maintained by Alex Coulton.