Multiple sequence alignment - TraesCS2B01G143600

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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 TraesCS2B01G143600 chr2B 100.000 3142 0 0 1 3142 110045295 110042154 0.000000e+00 5803.0
1 TraesCS2B01G143600 chr2B 90.950 1116 52 9 1019 2107 109963779 109964872 0.000000e+00 1456.0
2 TraesCS2B01G143600 chr2B 89.961 777 72 4 1336 2106 110370935 110371711 0.000000e+00 998.0
3 TraesCS2B01G143600 chr2B 89.318 777 77 3 1336 2106 110406395 110407171 0.000000e+00 970.0
4 TraesCS2B01G143600 chr2B 86.258 604 58 13 362 956 109955703 109956290 1.590000e-177 632.0
5 TraesCS2B01G143600 chr2B 95.714 70 3 0 952 1021 109961450 109961519 2.560000e-21 113.0
6 TraesCS2B01G143600 chr2B 100.000 43 0 0 2187 2229 23029052 23029094 2.600000e-11 80.5
7 TraesCS2B01G143600 chr2B 100.000 43 0 0 2187 2229 23029140 23029098 2.600000e-11 80.5
8 TraesCS2B01G143600 chr2B 95.918 49 2 0 2181 2229 536806442 536806394 2.600000e-11 80.5
9 TraesCS2B01G143600 chr2D 91.052 1777 106 25 414 2167 72595655 72593909 0.000000e+00 2351.0
10 TraesCS2B01G143600 chr2D 87.916 1291 79 38 362 1643 72772550 72771328 0.000000e+00 1448.0
11 TraesCS2B01G143600 chr2D 87.115 1071 100 21 1103 2167 23168476 23167438 0.000000e+00 1179.0
12 TraesCS2B01G143600 chr2D 89.704 777 74 4 1336 2106 72998927 72999703 0.000000e+00 987.0
13 TraesCS2B01G143600 chr2D 83.810 840 96 15 2310 3142 72771016 72770210 0.000000e+00 761.0
14 TraesCS2B01G143600 chr2D 85.899 695 65 11 2452 3142 72575558 72574893 0.000000e+00 710.0
15 TraesCS2B01G143600 chr2D 87.013 616 47 18 513 1120 593841049 593841639 0.000000e+00 664.0
16 TraesCS2B01G143600 chr2D 94.096 271 12 2 312 578 72595927 72595657 2.920000e-110 409.0
17 TraesCS2B01G143600 chr2D 88.550 262 29 1 2875 3136 72905245 72905505 1.820000e-82 316.0
18 TraesCS2B01G143600 chr2D 92.715 151 9 1 1 151 72605619 72605471 1.900000e-52 217.0
19 TraesCS2B01G143600 chr2D 90.654 107 8 2 195 300 72772823 72772718 1.170000e-29 141.0
20 TraesCS2B01G143600 chr2D 91.111 45 4 0 312 356 72772731 72772687 9.410000e-06 62.1
21 TraesCS2B01G143600 chrUn 89.701 1806 122 26 382 2167 287774510 287772749 0.000000e+00 2246.0
22 TraesCS2B01G143600 chrUn 89.701 1806 122 26 382 2167 297963635 297961874 0.000000e+00 2246.0
23 TraesCS2B01G143600 chr2A 89.436 1827 105 39 362 2164 71436528 71434766 0.000000e+00 2224.0
24 TraesCS2B01G143600 chr2A 89.189 777 77 5 1336 2106 71587239 71588014 0.000000e+00 963.0
25 TraesCS2B01G143600 chr2A 82.327 911 111 24 2239 3142 71434727 71433860 0.000000e+00 745.0
26 TraesCS2B01G143600 chr2A 88.785 107 10 2 195 300 71436804 71436699 2.540000e-26 130.0
27 TraesCS2B01G143600 chr2A 100.000 40 0 0 2187 2226 758265638 758265599 1.210000e-09 75.0
28 TraesCS2B01G143600 chr3D 83.784 148 23 1 2994 3141 4934779 4934925 4.230000e-29 139.0
29 TraesCS2B01G143600 chr3D 84.173 139 18 3 2874 3009 13690200 13690063 7.070000e-27 132.0
30 TraesCS2B01G143600 chr4D 84.286 140 19 3 2872 3009 464397039 464396901 1.970000e-27 134.0
31 TraesCS2B01G143600 chr4D 80.180 111 18 4 33 140 362129156 362129265 2.600000e-11 80.5
32 TraesCS2B01G143600 chr5D 82.877 146 22 3 2867 3009 378333342 378333197 9.150000e-26 128.0
33 TraesCS2B01G143600 chr5D 82.517 143 21 4 2872 3011 435890903 435891044 4.260000e-24 122.0
34 TraesCS2B01G143600 chr1D 84.496 129 18 2 2867 2995 83695424 83695298 3.290000e-25 126.0
35 TraesCS2B01G143600 chr3B 100.000 43 0 0 2187 2229 543846856 543846898 2.600000e-11 80.5
36 TraesCS2B01G143600 chr1A 100.000 43 0 0 2187 2229 27400111 27400069 2.600000e-11 80.5
37 TraesCS2B01G143600 chr7B 94.231 52 2 1 2177 2228 219584729 219584679 9.340000e-11 78.7
38 TraesCS2B01G143600 chr6A 95.833 48 2 0 2182 2229 33306658 33306611 9.340000e-11 78.7
39 TraesCS2B01G143600 chr6A 97.297 37 1 0 312 348 221350837 221350873 2.620000e-06 63.9
40 TraesCS2B01G143600 chr1B 92.308 52 3 1 2182 2232 381381746 381381695 4.350000e-09 73.1
41 TraesCS2B01G143600 chr6D 97.297 37 1 0 312 348 161977816 161977852 2.620000e-06 63.9
42 TraesCS2B01G143600 chr6B 97.297 37 1 0 312 348 300718104 300718068 2.620000e-06 63.9
43 TraesCS2B01G143600 chr6B 91.304 46 1 2 47 92 513618678 513618636 3.380000e-05 60.2


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 TraesCS2B01G143600 chr2B 110042154 110045295 3141 True 5803.000 5803 100.000000 1 3142 1 chr2B.!!$R2 3141
1 TraesCS2B01G143600 chr2B 110370935 110371711 776 False 998.000 998 89.961000 1336 2106 1 chr2B.!!$F3 770
2 TraesCS2B01G143600 chr2B 110406395 110407171 776 False 970.000 970 89.318000 1336 2106 1 chr2B.!!$F4 770
3 TraesCS2B01G143600 chr2B 109961450 109964872 3422 False 784.500 1456 93.332000 952 2107 2 chr2B.!!$F5 1155
4 TraesCS2B01G143600 chr2B 109955703 109956290 587 False 632.000 632 86.258000 362 956 1 chr2B.!!$F2 594
5 TraesCS2B01G143600 chr2D 72593909 72595927 2018 True 1380.000 2351 92.574000 312 2167 2 chr2D.!!$R4 1855
6 TraesCS2B01G143600 chr2D 23167438 23168476 1038 True 1179.000 1179 87.115000 1103 2167 1 chr2D.!!$R1 1064
7 TraesCS2B01G143600 chr2D 72998927 72999703 776 False 987.000 987 89.704000 1336 2106 1 chr2D.!!$F2 770
8 TraesCS2B01G143600 chr2D 72574893 72575558 665 True 710.000 710 85.899000 2452 3142 1 chr2D.!!$R2 690
9 TraesCS2B01G143600 chr2D 593841049 593841639 590 False 664.000 664 87.013000 513 1120 1 chr2D.!!$F3 607
10 TraesCS2B01G143600 chr2D 72770210 72772823 2613 True 603.025 1448 88.372750 195 3142 4 chr2D.!!$R5 2947
11 TraesCS2B01G143600 chrUn 287772749 287774510 1761 True 2246.000 2246 89.701000 382 2167 1 chrUn.!!$R1 1785
12 TraesCS2B01G143600 chrUn 297961874 297963635 1761 True 2246.000 2246 89.701000 382 2167 1 chrUn.!!$R2 1785
13 TraesCS2B01G143600 chr2A 71433860 71436804 2944 True 1033.000 2224 86.849333 195 3142 3 chr2A.!!$R2 2947
14 TraesCS2B01G143600 chr2A 71587239 71588014 775 False 963.000 963 89.189000 1336 2106 1 chr2A.!!$F1 770

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
105 106 0.106015 CCCTCCCACCCCAATCAATC 60.106 60.0 0.0 0.0 0.0 2.67 F
106 107 0.106015 CCTCCCACCCCAATCAATCC 60.106 60.0 0.0 0.0 0.0 3.01 F
927 1242 0.594602 TCACGACCGTACTGAACTGG 59.405 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 4265 1.343789 CGATGGAGTCCATGCTCATCT 59.656 52.381 29.6 2.95 45.26 2.90 R
1988 4718 2.204136 ACCTCCAGCACCATCCCA 60.204 61.111 0.0 0.00 0.00 4.37 R
2904 5659 0.165295 GCGTTCGGTTTAGCCTTCAC 59.835 55.000 0.0 0.00 34.25 3.18 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
25 26 7.708998 TGCTACACGTACATAATTCATCTACA 58.291 34.615 0.00 0.00 0.00 2.74
26 27 8.192110 TGCTACACGTACATAATTCATCTACAA 58.808 33.333 0.00 0.00 0.00 2.41
27 28 9.027129 GCTACACGTACATAATTCATCTACAAA 57.973 33.333 0.00 0.00 0.00 2.83
43 44 9.109393 TCATCTACAAAATCATAAGTAACCTGC 57.891 33.333 0.00 0.00 0.00 4.85
44 45 7.859325 TCTACAAAATCATAAGTAACCTGCC 57.141 36.000 0.00 0.00 0.00 4.85
45 46 7.630082 TCTACAAAATCATAAGTAACCTGCCT 58.370 34.615 0.00 0.00 0.00 4.75
46 47 8.764558 TCTACAAAATCATAAGTAACCTGCCTA 58.235 33.333 0.00 0.00 0.00 3.93
47 48 9.391006 CTACAAAATCATAAGTAACCTGCCTAA 57.609 33.333 0.00 0.00 0.00 2.69
48 49 8.823220 ACAAAATCATAAGTAACCTGCCTAAT 57.177 30.769 0.00 0.00 0.00 1.73
49 50 9.255029 ACAAAATCATAAGTAACCTGCCTAATT 57.745 29.630 0.00 0.00 0.00 1.40
58 59 8.966069 AAGTAACCTGCCTAATTAATTCTCTC 57.034 34.615 3.39 0.00 0.00 3.20
59 60 7.210873 AGTAACCTGCCTAATTAATTCTCTCG 58.789 38.462 3.39 0.00 0.00 4.04
60 61 4.962155 ACCTGCCTAATTAATTCTCTCGG 58.038 43.478 3.39 4.37 0.00 4.63
61 62 3.748568 CCTGCCTAATTAATTCTCTCGGC 59.251 47.826 3.39 10.34 36.85 5.54
62 63 3.740115 TGCCTAATTAATTCTCTCGGCC 58.260 45.455 3.39 0.00 35.51 6.13
63 64 3.391296 TGCCTAATTAATTCTCTCGGCCT 59.609 43.478 3.39 0.00 35.51 5.19
64 65 3.997681 GCCTAATTAATTCTCTCGGCCTC 59.002 47.826 3.39 0.00 0.00 4.70
65 66 4.570930 CCTAATTAATTCTCTCGGCCTCC 58.429 47.826 3.39 0.00 0.00 4.30
66 67 4.284746 CCTAATTAATTCTCTCGGCCTCCT 59.715 45.833 3.39 0.00 0.00 3.69
67 68 3.760580 ATTAATTCTCTCGGCCTCCTG 57.239 47.619 0.00 0.00 0.00 3.86
68 69 2.454336 TAATTCTCTCGGCCTCCTGA 57.546 50.000 0.00 0.00 0.00 3.86
69 70 1.799933 AATTCTCTCGGCCTCCTGAT 58.200 50.000 0.00 0.00 0.00 2.90
70 71 1.799933 ATTCTCTCGGCCTCCTGATT 58.200 50.000 0.00 0.00 0.00 2.57
71 72 1.573108 TTCTCTCGGCCTCCTGATTT 58.427 50.000 0.00 0.00 0.00 2.17
72 73 1.573108 TCTCTCGGCCTCCTGATTTT 58.427 50.000 0.00 0.00 0.00 1.82
73 74 1.482593 TCTCTCGGCCTCCTGATTTTC 59.517 52.381 0.00 0.00 0.00 2.29
74 75 1.208052 CTCTCGGCCTCCTGATTTTCA 59.792 52.381 0.00 0.00 0.00 2.69
75 76 1.066143 TCTCGGCCTCCTGATTTTCAC 60.066 52.381 0.00 0.00 0.00 3.18
76 77 0.391130 TCGGCCTCCTGATTTTCACG 60.391 55.000 0.00 0.00 0.00 4.35
77 78 1.369091 CGGCCTCCTGATTTTCACGG 61.369 60.000 0.00 0.00 0.00 4.94
78 79 1.032114 GGCCTCCTGATTTTCACGGG 61.032 60.000 0.00 0.00 35.32 5.28
79 80 0.322546 GCCTCCTGATTTTCACGGGT 60.323 55.000 0.00 0.00 35.49 5.28
80 81 1.453155 CCTCCTGATTTTCACGGGTG 58.547 55.000 0.00 0.00 35.49 4.61
81 82 1.271379 CCTCCTGATTTTCACGGGTGT 60.271 52.381 0.00 0.00 35.49 4.16
83 84 0.881118 CCTGATTTTCACGGGTGTGG 59.119 55.000 0.00 0.00 46.42 4.17
84 85 0.881118 CTGATTTTCACGGGTGTGGG 59.119 55.000 0.00 0.00 46.42 4.61
85 86 1.175983 TGATTTTCACGGGTGTGGGC 61.176 55.000 0.00 0.00 46.42 5.36
86 87 1.873270 GATTTTCACGGGTGTGGGCC 61.873 60.000 0.00 0.00 46.42 5.80
87 88 4.589675 TTTCACGGGTGTGGGCCC 62.590 66.667 17.59 17.59 46.42 5.80
101 102 4.143301 GCCCCTCCCACCCCAATC 62.143 72.222 0.00 0.00 0.00 2.67
102 103 2.616893 CCCCTCCCACCCCAATCA 60.617 66.667 0.00 0.00 0.00 2.57
103 104 2.245379 CCCCTCCCACCCCAATCAA 61.245 63.158 0.00 0.00 0.00 2.57
104 105 1.593166 CCCCTCCCACCCCAATCAAT 61.593 60.000 0.00 0.00 0.00 2.57
105 106 0.106015 CCCTCCCACCCCAATCAATC 60.106 60.000 0.00 0.00 0.00 2.67
106 107 0.106015 CCTCCCACCCCAATCAATCC 60.106 60.000 0.00 0.00 0.00 3.01
107 108 0.630673 CTCCCACCCCAATCAATCCA 59.369 55.000 0.00 0.00 0.00 3.41
108 109 1.006998 CTCCCACCCCAATCAATCCAA 59.993 52.381 0.00 0.00 0.00 3.53
109 110 1.650700 TCCCACCCCAATCAATCCAAT 59.349 47.619 0.00 0.00 0.00 3.16
110 111 2.041701 CCCACCCCAATCAATCCAATC 58.958 52.381 0.00 0.00 0.00 2.67
111 112 2.041701 CCACCCCAATCAATCCAATCC 58.958 52.381 0.00 0.00 0.00 3.01
112 113 2.041701 CACCCCAATCAATCCAATCCC 58.958 52.381 0.00 0.00 0.00 3.85
113 114 1.650700 ACCCCAATCAATCCAATCCCA 59.349 47.619 0.00 0.00 0.00 4.37
114 115 2.045605 ACCCCAATCAATCCAATCCCAA 59.954 45.455 0.00 0.00 0.00 4.12
115 116 2.701951 CCCCAATCAATCCAATCCCAAG 59.298 50.000 0.00 0.00 0.00 3.61
116 117 3.377573 CCCAATCAATCCAATCCCAAGT 58.622 45.455 0.00 0.00 0.00 3.16
117 118 3.385755 CCCAATCAATCCAATCCCAAGTC 59.614 47.826 0.00 0.00 0.00 3.01
118 119 4.284178 CCAATCAATCCAATCCCAAGTCT 58.716 43.478 0.00 0.00 0.00 3.24
119 120 4.340381 CCAATCAATCCAATCCCAAGTCTC 59.660 45.833 0.00 0.00 0.00 3.36
120 121 3.652057 TCAATCCAATCCCAAGTCTCC 57.348 47.619 0.00 0.00 0.00 3.71
121 122 2.918934 TCAATCCAATCCCAAGTCTCCA 59.081 45.455 0.00 0.00 0.00 3.86
122 123 3.528905 TCAATCCAATCCCAAGTCTCCAT 59.471 43.478 0.00 0.00 0.00 3.41
123 124 3.589951 ATCCAATCCCAAGTCTCCATG 57.410 47.619 0.00 0.00 0.00 3.66
124 125 2.278245 TCCAATCCCAAGTCTCCATGT 58.722 47.619 0.00 0.00 0.00 3.21
125 126 2.649312 TCCAATCCCAAGTCTCCATGTT 59.351 45.455 0.00 0.00 0.00 2.71
126 127 3.075882 TCCAATCCCAAGTCTCCATGTTT 59.924 43.478 0.00 0.00 0.00 2.83
127 128 3.834231 CCAATCCCAAGTCTCCATGTTTT 59.166 43.478 0.00 0.00 0.00 2.43
128 129 4.082026 CCAATCCCAAGTCTCCATGTTTTC 60.082 45.833 0.00 0.00 0.00 2.29
129 130 4.664688 ATCCCAAGTCTCCATGTTTTCT 57.335 40.909 0.00 0.00 0.00 2.52
130 131 5.779241 ATCCCAAGTCTCCATGTTTTCTA 57.221 39.130 0.00 0.00 0.00 2.10
131 132 5.779241 TCCCAAGTCTCCATGTTTTCTAT 57.221 39.130 0.00 0.00 0.00 1.98
132 133 5.745227 TCCCAAGTCTCCATGTTTTCTATC 58.255 41.667 0.00 0.00 0.00 2.08
133 134 5.250543 TCCCAAGTCTCCATGTTTTCTATCA 59.749 40.000 0.00 0.00 0.00 2.15
134 135 5.355350 CCCAAGTCTCCATGTTTTCTATCAC 59.645 44.000 0.00 0.00 0.00 3.06
135 136 5.063944 CCAAGTCTCCATGTTTTCTATCACG 59.936 44.000 0.00 0.00 0.00 4.35
136 137 5.407407 AGTCTCCATGTTTTCTATCACGT 57.593 39.130 0.00 0.00 0.00 4.49
137 138 6.525578 AGTCTCCATGTTTTCTATCACGTA 57.474 37.500 0.00 0.00 0.00 3.57
138 139 6.931838 AGTCTCCATGTTTTCTATCACGTAA 58.068 36.000 0.00 0.00 0.00 3.18
139 140 7.383687 AGTCTCCATGTTTTCTATCACGTAAA 58.616 34.615 0.00 0.00 0.00 2.01
140 141 7.876068 AGTCTCCATGTTTTCTATCACGTAAAA 59.124 33.333 0.00 0.00 0.00 1.52
141 142 8.500773 GTCTCCATGTTTTCTATCACGTAAAAA 58.499 33.333 0.00 0.00 0.00 1.94
142 143 8.500773 TCTCCATGTTTTCTATCACGTAAAAAC 58.499 33.333 11.97 11.97 40.37 2.43
143 144 7.586747 TCCATGTTTTCTATCACGTAAAAACC 58.413 34.615 14.39 0.04 39.63 3.27
144 145 7.228906 TCCATGTTTTCTATCACGTAAAAACCA 59.771 33.333 14.39 4.27 39.63 3.67
145 146 8.026607 CCATGTTTTCTATCACGTAAAAACCAT 58.973 33.333 14.39 5.80 39.63 3.55
148 149 9.275398 TGTTTTCTATCACGTAAAAACCATACT 57.725 29.630 14.39 0.00 39.63 2.12
152 153 9.715121 TTCTATCACGTAAAAACCATACTTTCT 57.285 29.630 0.00 0.00 0.00 2.52
242 243 9.523168 AAGTAGGTCTAGCATTACTCTAATAGG 57.477 37.037 0.00 0.00 0.00 2.57
245 246 6.957020 AGGTCTAGCATTACTCTAATAGGCAT 59.043 38.462 0.00 0.00 0.00 4.40
285 286 4.712122 TTTGGTGTCGCTTTTCTTTCTT 57.288 36.364 0.00 0.00 0.00 2.52
286 287 3.963383 TGGTGTCGCTTTTCTTTCTTC 57.037 42.857 0.00 0.00 0.00 2.87
287 288 3.541632 TGGTGTCGCTTTTCTTTCTTCT 58.458 40.909 0.00 0.00 0.00 2.85
288 289 3.312421 TGGTGTCGCTTTTCTTTCTTCTG 59.688 43.478 0.00 0.00 0.00 3.02
289 290 3.312697 GGTGTCGCTTTTCTTTCTTCTGT 59.687 43.478 0.00 0.00 0.00 3.41
290 291 4.201920 GGTGTCGCTTTTCTTTCTTCTGTT 60.202 41.667 0.00 0.00 0.00 3.16
291 292 5.007332 GGTGTCGCTTTTCTTTCTTCTGTTA 59.993 40.000 0.00 0.00 0.00 2.41
292 293 6.293462 GGTGTCGCTTTTCTTTCTTCTGTTAT 60.293 38.462 0.00 0.00 0.00 1.89
293 294 7.095355 GGTGTCGCTTTTCTTTCTTCTGTTATA 60.095 37.037 0.00 0.00 0.00 0.98
294 295 8.280497 GTGTCGCTTTTCTTTCTTCTGTTATAA 58.720 33.333 0.00 0.00 0.00 0.98
295 296 8.495949 TGTCGCTTTTCTTTCTTCTGTTATAAG 58.504 33.333 0.00 0.00 0.00 1.73
296 297 7.478978 GTCGCTTTTCTTTCTTCTGTTATAAGC 59.521 37.037 0.00 0.00 0.00 3.09
297 298 7.172532 TCGCTTTTCTTTCTTCTGTTATAAGCA 59.827 33.333 0.00 0.00 35.29 3.91
298 299 7.965107 CGCTTTTCTTTCTTCTGTTATAAGCAT 59.035 33.333 0.00 0.00 35.29 3.79
299 300 9.631452 GCTTTTCTTTCTTCTGTTATAAGCATT 57.369 29.630 0.00 0.00 35.57 3.56
380 515 6.097696 AGAGAGTATTTCTTTACAGAGGGAGC 59.902 42.308 0.00 0.00 35.87 4.70
484 621 4.159244 AGTGTGGTTTGGTTTGTAGCTA 57.841 40.909 0.00 0.00 0.00 3.32
493 630 5.748670 TTGGTTTGTAGCTACATGGACTA 57.251 39.130 26.54 18.93 35.89 2.59
494 631 5.080969 TGGTTTGTAGCTACATGGACTAC 57.919 43.478 26.54 16.09 35.89 2.73
564 867 4.689612 ATGTCCTGCGTTTATGACCTAT 57.310 40.909 0.00 0.00 0.00 2.57
607 912 9.500785 TCTTTTCATTTTGGTTGAGTTTTCTTT 57.499 25.926 0.00 0.00 0.00 2.52
649 956 8.407832 TCAGTCAGCACCAATATTTTGATTATG 58.592 33.333 0.00 0.00 34.60 1.90
651 958 8.408601 AGTCAGCACCAATATTTTGATTATGTC 58.591 33.333 0.00 0.00 34.60 3.06
681 989 9.917887 ATTAGGTATAGCCGTATAGATAGTTGT 57.082 33.333 0.00 0.00 43.70 3.32
723 1035 6.373774 AGAGATCAAATCTTCGCTTTCACATT 59.626 34.615 0.00 0.00 40.38 2.71
794 1109 1.176527 CAATACCCACCAGTGCCAAG 58.823 55.000 0.00 0.00 0.00 3.61
830 1145 0.807496 GCTGAAGATTCACCCACTGC 59.193 55.000 0.00 0.00 32.90 4.40
927 1242 0.594602 TCACGACCGTACTGAACTGG 59.405 55.000 0.00 0.00 0.00 4.00
979 1306 2.030185 CACAAGCAAATCAGCAGAGCTT 60.030 45.455 0.00 0.00 45.54 3.74
1038 3627 2.038557 GCACCACCTTCTTCTGAGGTAA 59.961 50.000 0.00 0.00 34.10 2.85
1044 3633 7.070074 CACCACCTTCTTCTGAGGTAATAGTAT 59.930 40.741 0.00 0.00 34.10 2.12
1045 3634 7.624077 ACCACCTTCTTCTGAGGTAATAGTATT 59.376 37.037 0.17 0.17 34.10 1.89
1154 3776 1.889573 GGTAAGATGAGCGCTGCCC 60.890 63.158 18.48 0.00 0.00 5.36
1275 3905 4.402056 TCTCTTCTTGGTTCTCGTTTGT 57.598 40.909 0.00 0.00 0.00 2.83
1277 3907 2.612212 TCTTCTTGGTTCTCGTTTGTGC 59.388 45.455 0.00 0.00 0.00 4.57
1278 3908 1.305201 TCTTGGTTCTCGTTTGTGCC 58.695 50.000 0.00 0.00 0.00 5.01
1367 4014 2.125673 GTGTCCGTCATCACCGGG 60.126 66.667 6.32 0.00 45.51 5.73
1623 4282 1.487976 GGAAGATGAGCATGGACTCCA 59.512 52.381 0.00 0.00 38.19 3.86
1988 4718 1.224592 GGGCATGAACGAGATGGGT 59.775 57.895 0.00 0.00 0.00 4.51
2145 4878 0.664767 GGTGACGAGTGAGTGACAGC 60.665 60.000 0.00 0.00 29.74 4.40
2167 4901 2.406401 GCATGGCATGACAGCGAC 59.594 61.111 30.69 7.44 34.64 5.19
2169 4903 1.721664 GCATGGCATGACAGCGACAT 61.722 55.000 30.69 0.00 34.64 3.06
2170 4904 0.306840 CATGGCATGACAGCGACATC 59.693 55.000 22.91 0.00 34.64 3.06
2171 4905 0.816825 ATGGCATGACAGCGACATCC 60.817 55.000 7.63 0.00 34.64 3.51
2173 4907 1.026182 GGCATGACAGCGACATCCAA 61.026 55.000 0.00 0.00 34.64 3.53
2174 4908 0.804364 GCATGACAGCGACATCCAAA 59.196 50.000 0.00 0.00 0.00 3.28
2183 4928 1.195900 GCGACATCCAAACAAGCGTAA 59.804 47.619 0.00 0.00 0.00 3.18
2187 4932 4.403453 GACATCCAAACAAGCGTAATGAC 58.597 43.478 0.00 0.00 0.00 3.06
2188 4933 4.072131 ACATCCAAACAAGCGTAATGACT 58.928 39.130 0.00 0.00 0.00 3.41
2189 4934 5.242434 ACATCCAAACAAGCGTAATGACTA 58.758 37.500 0.00 0.00 0.00 2.59
2190 4935 5.121768 ACATCCAAACAAGCGTAATGACTAC 59.878 40.000 0.00 0.00 0.00 2.73
2191 4936 4.890088 TCCAAACAAGCGTAATGACTACT 58.110 39.130 0.00 0.00 0.00 2.57
2192 4937 4.927425 TCCAAACAAGCGTAATGACTACTC 59.073 41.667 0.00 0.00 0.00 2.59
2193 4938 4.092968 CCAAACAAGCGTAATGACTACTCC 59.907 45.833 0.00 0.00 0.00 3.85
2194 4939 3.521947 ACAAGCGTAATGACTACTCCC 57.478 47.619 0.00 0.00 0.00 4.30
2195 4940 3.097614 ACAAGCGTAATGACTACTCCCT 58.902 45.455 0.00 0.00 0.00 4.20
2196 4941 3.130693 ACAAGCGTAATGACTACTCCCTC 59.869 47.826 0.00 0.00 0.00 4.30
2197 4942 3.300239 AGCGTAATGACTACTCCCTCT 57.700 47.619 0.00 0.00 0.00 3.69
2198 4943 2.952978 AGCGTAATGACTACTCCCTCTG 59.047 50.000 0.00 0.00 0.00 3.35
2199 4944 2.688958 GCGTAATGACTACTCCCTCTGT 59.311 50.000 0.00 0.00 0.00 3.41
2200 4945 3.881688 GCGTAATGACTACTCCCTCTGTA 59.118 47.826 0.00 0.00 0.00 2.74
2201 4946 4.261114 GCGTAATGACTACTCCCTCTGTAC 60.261 50.000 0.00 0.00 0.00 2.90
2202 4947 4.275443 CGTAATGACTACTCCCTCTGTACC 59.725 50.000 0.00 0.00 0.00 3.34
2203 4948 2.414994 TGACTACTCCCTCTGTACCG 57.585 55.000 0.00 0.00 0.00 4.02
2204 4949 1.911357 TGACTACTCCCTCTGTACCGA 59.089 52.381 0.00 0.00 0.00 4.69
2205 4950 2.306805 TGACTACTCCCTCTGTACCGAA 59.693 50.000 0.00 0.00 0.00 4.30
2206 4951 3.245016 TGACTACTCCCTCTGTACCGAAA 60.245 47.826 0.00 0.00 0.00 3.46
2207 4952 3.952967 GACTACTCCCTCTGTACCGAAAT 59.047 47.826 0.00 0.00 0.00 2.17
2208 4953 5.121380 ACTACTCCCTCTGTACCGAAATA 57.879 43.478 0.00 0.00 0.00 1.40
2209 4954 4.886489 ACTACTCCCTCTGTACCGAAATAC 59.114 45.833 0.00 0.00 0.00 1.89
2210 4955 3.705051 ACTCCCTCTGTACCGAAATACA 58.295 45.455 0.00 0.00 33.96 2.29
2211 4956 4.287552 ACTCCCTCTGTACCGAAATACAT 58.712 43.478 0.00 0.00 34.59 2.29
2212 4957 4.099573 ACTCCCTCTGTACCGAAATACATG 59.900 45.833 0.00 0.00 34.59 3.21
2213 4958 4.028131 TCCCTCTGTACCGAAATACATGT 58.972 43.478 2.69 2.69 34.59 3.21
2214 4959 4.098960 TCCCTCTGTACCGAAATACATGTC 59.901 45.833 0.00 0.00 34.59 3.06
2215 4960 4.042398 CCTCTGTACCGAAATACATGTCG 58.958 47.826 0.00 0.00 34.59 4.35
2216 4961 3.441163 TCTGTACCGAAATACATGTCGC 58.559 45.455 0.00 0.00 34.59 5.19
2217 4962 3.129813 TCTGTACCGAAATACATGTCGCT 59.870 43.478 0.00 0.00 34.59 4.93
2218 4963 3.183754 TGTACCGAAATACATGTCGCTG 58.816 45.455 0.00 0.00 35.93 5.18
2219 4964 1.651987 ACCGAAATACATGTCGCTGG 58.348 50.000 0.00 1.83 35.93 4.85
2220 4965 1.206132 ACCGAAATACATGTCGCTGGA 59.794 47.619 0.00 0.00 35.93 3.86
2221 4966 1.860950 CCGAAATACATGTCGCTGGAG 59.139 52.381 0.00 0.00 35.93 3.86
2222 4967 2.540515 CGAAATACATGTCGCTGGAGT 58.459 47.619 0.00 0.00 0.00 3.85
2223 4968 3.490249 CCGAAATACATGTCGCTGGAGTA 60.490 47.826 0.00 0.00 35.93 2.59
2224 4969 3.731216 CGAAATACATGTCGCTGGAGTAG 59.269 47.826 0.00 0.00 0.00 2.57
2235 4980 2.906691 CTGGAGTAGCTGATTGGGAG 57.093 55.000 0.00 0.00 0.00 4.30
2236 4981 2.114616 CTGGAGTAGCTGATTGGGAGT 58.885 52.381 0.00 0.00 0.00 3.85
2237 4982 3.300388 CTGGAGTAGCTGATTGGGAGTA 58.700 50.000 0.00 0.00 0.00 2.59
2273 5018 3.129113 ACAGCATGCGCAATAAATTCAGA 59.871 39.130 17.11 0.00 42.53 3.27
2278 5023 6.314400 AGCATGCGCAATAAATTCAGAAAAAT 59.686 30.769 17.11 0.00 42.27 1.82
2290 5035 8.532977 AAATTCAGAAAAATTAATGGACGTGG 57.467 30.769 0.00 0.00 0.00 4.94
2291 5036 5.637006 TCAGAAAAATTAATGGACGTGGG 57.363 39.130 0.00 0.00 0.00 4.61
2293 5038 3.829601 AGAAAAATTAATGGACGTGGGCA 59.170 39.130 0.00 0.00 0.00 5.36
2294 5039 3.586100 AAAATTAATGGACGTGGGCAC 57.414 42.857 0.00 0.00 0.00 5.01
2321 5066 5.529430 CCGTTAGGGCAATGTATAATTGTGA 59.471 40.000 0.51 0.00 0.00 3.58
2325 5070 8.413229 GTTAGGGCAATGTATAATTGTGACATT 58.587 33.333 8.02 8.02 42.97 2.71
2356 5101 8.874156 AGATGACACATAGGATAAATGCTAAGA 58.126 33.333 1.48 0.00 34.35 2.10
2370 5115 6.999705 AATGCTAAGATGGAGAAGAGAGAT 57.000 37.500 0.00 0.00 0.00 2.75
2424 5170 8.668510 TTTGAGAGATGATTCCTTAGCATAAC 57.331 34.615 0.00 0.00 0.00 1.89
2436 5182 8.662781 TTCCTTAGCATAACATGTCTAATCAC 57.337 34.615 0.00 0.00 32.54 3.06
2501 5247 8.554011 AGATAACCCATTTTAGGCTTGTACTTA 58.446 33.333 0.00 0.00 0.00 2.24
2502 5248 9.350951 GATAACCCATTTTAGGCTTGTACTTAT 57.649 33.333 0.00 0.00 0.00 1.73
2503 5249 9.709387 ATAACCCATTTTAGGCTTGTACTTATT 57.291 29.630 0.00 0.00 0.00 1.40
2504 5250 7.404671 ACCCATTTTAGGCTTGTACTTATTG 57.595 36.000 0.00 0.00 0.00 1.90
2505 5251 6.951778 ACCCATTTTAGGCTTGTACTTATTGT 59.048 34.615 0.00 0.00 0.00 2.71
2506 5252 7.122204 ACCCATTTTAGGCTTGTACTTATTGTC 59.878 37.037 0.00 0.00 0.00 3.18
2571 5317 9.494271 ACGATCTTATTAATCATTGTACATGCT 57.506 29.630 0.00 0.00 0.00 3.79
2599 5345 3.966979 TCTTGATATGTGGGTGCATGTT 58.033 40.909 0.00 0.00 0.00 2.71
2628 5375 3.057174 CCGCCTAACACAATTTGCCTTTA 60.057 43.478 0.00 0.00 0.00 1.85
2651 5398 6.932901 ATTTTCAACAATGCTACATTCACG 57.067 33.333 0.00 0.00 0.00 4.35
2652 5399 4.418013 TTCAACAATGCTACATTCACGG 57.582 40.909 0.00 0.00 0.00 4.94
2653 5400 3.669536 TCAACAATGCTACATTCACGGA 58.330 40.909 0.00 0.00 0.00 4.69
2654 5401 3.684305 TCAACAATGCTACATTCACGGAG 59.316 43.478 0.00 0.00 0.00 4.63
2655 5402 2.632377 ACAATGCTACATTCACGGAGG 58.368 47.619 0.00 0.00 0.00 4.30
2656 5403 2.236146 ACAATGCTACATTCACGGAGGA 59.764 45.455 0.00 0.00 0.00 3.71
2657 5404 2.868583 CAATGCTACATTCACGGAGGAG 59.131 50.000 0.00 0.00 0.00 3.69
2658 5405 1.557099 TGCTACATTCACGGAGGAGT 58.443 50.000 0.00 0.00 0.00 3.85
2659 5406 2.730382 TGCTACATTCACGGAGGAGTA 58.270 47.619 0.00 0.00 0.00 2.59
2660 5407 2.426024 TGCTACATTCACGGAGGAGTAC 59.574 50.000 0.00 0.00 0.00 2.73
2661 5408 2.688958 GCTACATTCACGGAGGAGTACT 59.311 50.000 0.00 0.00 0.00 2.73
2662 5409 3.243134 GCTACATTCACGGAGGAGTACTC 60.243 52.174 14.87 14.87 45.84 2.59
2678 5425 5.069501 AGTACTCTTCACGGAATAACACC 57.930 43.478 0.00 0.00 0.00 4.16
2679 5426 4.525487 AGTACTCTTCACGGAATAACACCA 59.475 41.667 0.00 0.00 0.00 4.17
2689 5437 4.073549 CGGAATAACACCAGGGTTTTACA 58.926 43.478 0.00 0.00 32.29 2.41
2713 5461 4.585879 AGTGTTTGTGACTTGTTAGGTGT 58.414 39.130 0.00 0.00 0.00 4.16
2733 5481 5.339200 GGTGTTGATTGGATTAAGGGAGAGA 60.339 44.000 0.00 0.00 0.00 3.10
2740 5488 2.615391 GATTAAGGGAGAGAGAGGGGG 58.385 57.143 0.00 0.00 0.00 5.40
2758 5506 0.835971 GGCCCACCCACCTGAAAATT 60.836 55.000 0.00 0.00 0.00 1.82
2760 5508 1.548719 GCCCACCCACCTGAAAATTAC 59.451 52.381 0.00 0.00 0.00 1.89
2761 5509 1.816224 CCCACCCACCTGAAAATTACG 59.184 52.381 0.00 0.00 0.00 3.18
2783 5533 4.081087 CGGGGGTTGAAGAGAATTAGAAGA 60.081 45.833 0.00 0.00 0.00 2.87
2790 5540 6.126863 TGAAGAGAATTAGAAGAAAGGGCA 57.873 37.500 0.00 0.00 0.00 5.36
2877 5632 5.884792 AGGCTCATCGAGATTTGAGAAAAAT 59.115 36.000 16.11 0.00 41.53 1.82
2904 5659 6.428771 TCCAAAATAAACCTTGAACTCGTAGG 59.571 38.462 0.00 0.00 35.14 3.18
2905 5660 6.206048 CCAAAATAAACCTTGAACTCGTAGGT 59.794 38.462 0.00 0.00 43.98 3.08
2916 5671 3.589495 ACTCGTAGGTGAAGGCTAAAC 57.411 47.619 0.00 0.00 0.00 2.01
2925 5680 1.084289 GAAGGCTAAACCGAACGCAT 58.916 50.000 0.00 0.00 46.52 4.73
2932 5687 4.469552 GCTAAACCGAACGCATAAGTTTT 58.530 39.130 0.00 0.00 34.00 2.43
2986 5741 6.310941 TGATCCAGGTCAATTTTGAACCTTA 58.689 36.000 4.75 2.08 45.96 2.69
2989 5744 5.538433 TCCAGGTCAATTTTGAACCTTAAGG 59.462 40.000 20.42 20.42 45.96 2.69
2992 5747 4.039852 GGTCAATTTTGAACCTTAAGGGCA 59.960 41.667 25.31 18.91 38.96 5.36
3040 5795 0.457443 TCGATCTGCATCTGAACGCT 59.543 50.000 0.00 0.00 30.60 5.07
3043 5798 2.796032 CGATCTGCATCTGAACGCTACA 60.796 50.000 0.00 0.00 0.00 2.74
3086 5842 7.149192 CGCGAACCATGTTTTTCTTTTTAGTAG 60.149 37.037 0.00 0.00 0.00 2.57
3137 5899 0.108138 ACTCACATTGCGACCTAGCC 60.108 55.000 0.00 0.00 36.02 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.708998 TGTAGATGAATTATGTACGTGTAGCA 58.291 34.615 0.00 0.00 38.13 3.49
1 2 8.570096 TTGTAGATGAATTATGTACGTGTAGC 57.430 34.615 0.00 0.00 38.13 3.58
17 18 9.109393 GCAGGTTACTTATGATTTTGTAGATGA 57.891 33.333 0.00 0.00 0.00 2.92
18 19 8.345565 GGCAGGTTACTTATGATTTTGTAGATG 58.654 37.037 0.00 0.00 0.00 2.90
19 20 8.275040 AGGCAGGTTACTTATGATTTTGTAGAT 58.725 33.333 0.00 0.00 0.00 1.98
20 21 7.630082 AGGCAGGTTACTTATGATTTTGTAGA 58.370 34.615 0.00 0.00 0.00 2.59
21 22 7.865706 AGGCAGGTTACTTATGATTTTGTAG 57.134 36.000 0.00 0.00 0.00 2.74
22 23 9.914834 ATTAGGCAGGTTACTTATGATTTTGTA 57.085 29.630 0.00 0.00 0.00 2.41
23 24 8.823220 ATTAGGCAGGTTACTTATGATTTTGT 57.177 30.769 0.00 0.00 0.00 2.83
33 34 7.711339 CGAGAGAATTAATTAGGCAGGTTACTT 59.289 37.037 0.00 0.00 0.00 2.24
34 35 7.210873 CGAGAGAATTAATTAGGCAGGTTACT 58.789 38.462 0.00 0.00 0.00 2.24
35 36 6.424207 CCGAGAGAATTAATTAGGCAGGTTAC 59.576 42.308 0.00 0.00 0.00 2.50
36 37 6.522054 CCGAGAGAATTAATTAGGCAGGTTA 58.478 40.000 0.00 0.00 0.00 2.85
37 38 5.368989 CCGAGAGAATTAATTAGGCAGGTT 58.631 41.667 0.00 0.00 0.00 3.50
38 39 4.743955 GCCGAGAGAATTAATTAGGCAGGT 60.744 45.833 18.20 0.00 42.57 4.00
39 40 3.748568 GCCGAGAGAATTAATTAGGCAGG 59.251 47.826 18.20 13.04 42.57 4.85
40 41 3.748568 GGCCGAGAGAATTAATTAGGCAG 59.251 47.826 21.64 8.48 44.62 4.85
41 42 3.391296 AGGCCGAGAGAATTAATTAGGCA 59.609 43.478 21.64 0.00 44.62 4.75
42 43 3.997681 GAGGCCGAGAGAATTAATTAGGC 59.002 47.826 16.31 16.31 42.32 3.93
43 44 4.284746 AGGAGGCCGAGAGAATTAATTAGG 59.715 45.833 0.00 1.88 0.00 2.69
44 45 5.011125 TCAGGAGGCCGAGAGAATTAATTAG 59.989 44.000 0.00 0.00 0.00 1.73
45 46 4.899457 TCAGGAGGCCGAGAGAATTAATTA 59.101 41.667 0.00 0.00 0.00 1.40
46 47 3.711704 TCAGGAGGCCGAGAGAATTAATT 59.288 43.478 0.00 0.00 0.00 1.40
47 48 3.309296 TCAGGAGGCCGAGAGAATTAAT 58.691 45.455 0.00 0.00 0.00 1.40
48 49 2.747177 TCAGGAGGCCGAGAGAATTAA 58.253 47.619 0.00 0.00 0.00 1.40
49 50 2.454336 TCAGGAGGCCGAGAGAATTA 57.546 50.000 0.00 0.00 0.00 1.40
50 51 1.799933 ATCAGGAGGCCGAGAGAATT 58.200 50.000 0.00 0.00 0.00 2.17
51 52 1.799933 AATCAGGAGGCCGAGAGAAT 58.200 50.000 0.00 0.00 0.00 2.40
52 53 1.573108 AAATCAGGAGGCCGAGAGAA 58.427 50.000 0.00 0.00 0.00 2.87
53 54 1.482593 GAAAATCAGGAGGCCGAGAGA 59.517 52.381 0.00 0.00 0.00 3.10
54 55 1.208052 TGAAAATCAGGAGGCCGAGAG 59.792 52.381 0.00 0.00 0.00 3.20
55 56 1.066143 GTGAAAATCAGGAGGCCGAGA 60.066 52.381 0.00 0.00 0.00 4.04
56 57 1.373570 GTGAAAATCAGGAGGCCGAG 58.626 55.000 0.00 0.00 0.00 4.63
57 58 0.391130 CGTGAAAATCAGGAGGCCGA 60.391 55.000 0.00 0.00 34.44 5.54
58 59 1.369091 CCGTGAAAATCAGGAGGCCG 61.369 60.000 0.00 0.00 34.44 6.13
59 60 1.032114 CCCGTGAAAATCAGGAGGCC 61.032 60.000 0.00 0.00 34.44 5.19
60 61 0.322546 ACCCGTGAAAATCAGGAGGC 60.323 55.000 1.88 0.00 34.44 4.70
61 62 1.271379 ACACCCGTGAAAATCAGGAGG 60.271 52.381 0.96 4.44 34.44 4.30
62 63 1.806542 CACACCCGTGAAAATCAGGAG 59.193 52.381 0.96 0.00 46.80 3.69
63 64 1.544537 CCACACCCGTGAAAATCAGGA 60.545 52.381 0.96 0.00 46.80 3.86
64 65 0.881118 CCACACCCGTGAAAATCAGG 59.119 55.000 0.96 0.00 46.80 3.86
65 66 0.881118 CCCACACCCGTGAAAATCAG 59.119 55.000 0.96 0.00 46.80 2.90
66 67 1.175983 GCCCACACCCGTGAAAATCA 61.176 55.000 0.96 0.00 46.80 2.57
67 68 1.584495 GCCCACACCCGTGAAAATC 59.416 57.895 0.96 0.00 46.80 2.17
68 69 1.906333 GGCCCACACCCGTGAAAAT 60.906 57.895 0.96 0.00 46.80 1.82
69 70 2.519780 GGCCCACACCCGTGAAAA 60.520 61.111 0.96 0.00 46.80 2.29
70 71 4.589675 GGGCCCACACCCGTGAAA 62.590 66.667 19.95 0.00 46.80 2.69
84 85 4.143301 GATTGGGGTGGGAGGGGC 62.143 72.222 0.00 0.00 0.00 5.80
85 86 1.593166 ATTGATTGGGGTGGGAGGGG 61.593 60.000 0.00 0.00 0.00 4.79
86 87 0.106015 GATTGATTGGGGTGGGAGGG 60.106 60.000 0.00 0.00 0.00 4.30
87 88 0.106015 GGATTGATTGGGGTGGGAGG 60.106 60.000 0.00 0.00 0.00 4.30
88 89 0.630673 TGGATTGATTGGGGTGGGAG 59.369 55.000 0.00 0.00 0.00 4.30
89 90 1.088269 TTGGATTGATTGGGGTGGGA 58.912 50.000 0.00 0.00 0.00 4.37
90 91 2.041701 GATTGGATTGATTGGGGTGGG 58.958 52.381 0.00 0.00 0.00 4.61
91 92 2.041701 GGATTGGATTGATTGGGGTGG 58.958 52.381 0.00 0.00 0.00 4.61
92 93 2.041701 GGGATTGGATTGATTGGGGTG 58.958 52.381 0.00 0.00 0.00 4.61
93 94 1.650700 TGGGATTGGATTGATTGGGGT 59.349 47.619 0.00 0.00 0.00 4.95
94 95 2.475339 TGGGATTGGATTGATTGGGG 57.525 50.000 0.00 0.00 0.00 4.96
95 96 3.377573 ACTTGGGATTGGATTGATTGGG 58.622 45.455 0.00 0.00 0.00 4.12
96 97 4.284178 AGACTTGGGATTGGATTGATTGG 58.716 43.478 0.00 0.00 0.00 3.16
97 98 4.340381 GGAGACTTGGGATTGGATTGATTG 59.660 45.833 0.00 0.00 0.00 2.67
98 99 4.017222 TGGAGACTTGGGATTGGATTGATT 60.017 41.667 0.00 0.00 0.00 2.57
99 100 3.528905 TGGAGACTTGGGATTGGATTGAT 59.471 43.478 0.00 0.00 0.00 2.57
100 101 2.918934 TGGAGACTTGGGATTGGATTGA 59.081 45.455 0.00 0.00 0.00 2.57
101 102 3.370840 TGGAGACTTGGGATTGGATTG 57.629 47.619 0.00 0.00 0.00 2.67
102 103 3.270433 ACATGGAGACTTGGGATTGGATT 59.730 43.478 0.00 0.00 39.68 3.01
103 104 2.854967 ACATGGAGACTTGGGATTGGAT 59.145 45.455 0.00 0.00 39.68 3.41
104 105 2.278245 ACATGGAGACTTGGGATTGGA 58.722 47.619 0.00 0.00 39.68 3.53
105 106 2.814805 ACATGGAGACTTGGGATTGG 57.185 50.000 0.00 0.00 39.68 3.16
106 107 4.768968 AGAAAACATGGAGACTTGGGATTG 59.231 41.667 0.00 0.00 39.68 2.67
107 108 5.003096 AGAAAACATGGAGACTTGGGATT 57.997 39.130 0.00 0.00 39.68 3.01
108 109 4.664688 AGAAAACATGGAGACTTGGGAT 57.335 40.909 0.00 0.00 39.68 3.85
109 110 5.250543 TGATAGAAAACATGGAGACTTGGGA 59.749 40.000 0.00 0.00 39.68 4.37
110 111 5.355350 GTGATAGAAAACATGGAGACTTGGG 59.645 44.000 0.00 0.00 39.68 4.12
111 112 5.063944 CGTGATAGAAAACATGGAGACTTGG 59.936 44.000 0.00 0.00 39.68 3.61
112 113 5.639506 ACGTGATAGAAAACATGGAGACTTG 59.360 40.000 0.00 0.00 41.07 3.16
113 114 5.794894 ACGTGATAGAAAACATGGAGACTT 58.205 37.500 0.00 0.00 0.00 3.01
114 115 5.407407 ACGTGATAGAAAACATGGAGACT 57.593 39.130 0.00 0.00 0.00 3.24
115 116 7.591006 TTTACGTGATAGAAAACATGGAGAC 57.409 36.000 0.00 0.00 0.00 3.36
116 117 8.500773 GTTTTTACGTGATAGAAAACATGGAGA 58.499 33.333 0.00 0.00 40.12 3.71
117 118 7.749126 GGTTTTTACGTGATAGAAAACATGGAG 59.251 37.037 18.51 0.00 41.40 3.86
118 119 7.228906 TGGTTTTTACGTGATAGAAAACATGGA 59.771 33.333 18.51 0.00 41.40 3.41
119 120 7.364200 TGGTTTTTACGTGATAGAAAACATGG 58.636 34.615 18.51 0.00 41.40 3.66
120 121 8.964420 ATGGTTTTTACGTGATAGAAAACATG 57.036 30.769 18.51 0.00 41.45 3.21
122 123 9.275398 AGTATGGTTTTTACGTGATAGAAAACA 57.725 29.630 18.51 10.45 38.53 2.83
126 127 9.715121 AGAAAGTATGGTTTTTACGTGATAGAA 57.285 29.630 0.00 0.00 0.00 2.10
166 167 5.027737 TTTTCTCGAAAACGCATATCATGC 58.972 37.500 0.95 0.95 42.43 4.06
190 191 7.917720 AAGTAACGCATGATTTTACGTTTTT 57.082 28.000 10.92 5.27 45.62 1.94
191 192 7.917720 AAAGTAACGCATGATTTTACGTTTT 57.082 28.000 10.92 0.14 45.62 2.43
192 193 9.109533 CTTAAAGTAACGCATGATTTTACGTTT 57.890 29.630 10.92 10.53 45.62 3.60
194 195 7.799784 ACTTAAAGTAACGCATGATTTTACGT 58.200 30.769 0.00 0.00 41.16 3.57
195 196 9.405083 CTACTTAAAGTAACGCATGATTTTACG 57.595 33.333 0.00 0.00 32.08 3.18
196 197 9.698617 CCTACTTAAAGTAACGCATGATTTTAC 57.301 33.333 0.00 0.07 29.00 2.01
197 198 9.439500 ACCTACTTAAAGTAACGCATGATTTTA 57.561 29.630 0.00 0.00 29.00 1.52
198 199 8.331730 ACCTACTTAAAGTAACGCATGATTTT 57.668 30.769 0.00 0.00 29.00 1.82
199 200 7.822822 AGACCTACTTAAAGTAACGCATGATTT 59.177 33.333 0.00 0.00 29.00 2.17
200 201 7.328737 AGACCTACTTAAAGTAACGCATGATT 58.671 34.615 0.00 0.00 29.00 2.57
201 202 6.875076 AGACCTACTTAAAGTAACGCATGAT 58.125 36.000 0.00 0.00 29.00 2.45
202 203 6.276832 AGACCTACTTAAAGTAACGCATGA 57.723 37.500 0.00 0.00 29.00 3.07
206 207 5.644644 TGCTAGACCTACTTAAAGTAACGC 58.355 41.667 0.00 0.00 29.00 4.84
268 269 4.537936 ACAGAAGAAAGAAAAGCGACAC 57.462 40.909 0.00 0.00 0.00 3.67
269 270 6.861065 ATAACAGAAGAAAGAAAAGCGACA 57.139 33.333 0.00 0.00 0.00 4.35
272 273 7.298122 TGCTTATAACAGAAGAAAGAAAAGCG 58.702 34.615 0.00 0.00 38.69 4.68
300 301 2.094442 GCTTATAACAGCCCCGCAAAAA 60.094 45.455 0.00 0.00 33.21 1.94
301 302 1.474879 GCTTATAACAGCCCCGCAAAA 59.525 47.619 0.00 0.00 33.21 2.44
302 303 1.099689 GCTTATAACAGCCCCGCAAA 58.900 50.000 0.00 0.00 33.21 3.68
303 304 0.034960 TGCTTATAACAGCCCCGCAA 60.035 50.000 0.00 0.00 39.25 4.85
304 305 0.182537 ATGCTTATAACAGCCCCGCA 59.817 50.000 0.00 0.00 39.25 5.69
305 306 1.001378 CAATGCTTATAACAGCCCCGC 60.001 52.381 0.00 0.00 39.25 6.13
306 307 2.571212 TCAATGCTTATAACAGCCCCG 58.429 47.619 0.00 0.00 39.25 5.73
307 308 4.342092 ACAATCAATGCTTATAACAGCCCC 59.658 41.667 0.00 0.00 39.25 5.80
308 309 5.520376 ACAATCAATGCTTATAACAGCCC 57.480 39.130 0.00 0.00 39.25 5.19
309 310 5.979517 GGAACAATCAATGCTTATAACAGCC 59.020 40.000 0.00 0.00 39.25 4.85
310 311 6.799512 AGGAACAATCAATGCTTATAACAGC 58.200 36.000 0.00 0.00 40.55 4.40
356 357 6.127310 TGCTCCCTCTGTAAAGAAATACTCTC 60.127 42.308 0.00 0.00 31.02 3.20
357 358 5.721960 TGCTCCCTCTGTAAAGAAATACTCT 59.278 40.000 0.00 0.00 35.13 3.24
358 359 5.978814 TGCTCCCTCTGTAAAGAAATACTC 58.021 41.667 0.00 0.00 0.00 2.59
380 515 1.934589 TCACGACGCCCTGATTTATG 58.065 50.000 0.00 0.00 0.00 1.90
484 621 9.295825 TGAAAACATATTTCTTGTAGTCCATGT 57.704 29.630 2.98 0.00 0.00 3.21
607 912 6.048509 GCTGACTGAAAATCCAAAAGGAAAA 58.951 36.000 0.00 0.00 0.00 2.29
611 916 4.301628 GTGCTGACTGAAAATCCAAAAGG 58.698 43.478 0.00 0.00 0.00 3.11
626 933 8.190122 TGACATAATCAAAATATTGGTGCTGAC 58.810 33.333 0.00 0.00 37.15 3.51
662 969 9.956640 AAGTAGTACAACTATCTATACGGCTAT 57.043 33.333 2.52 0.00 32.65 2.97
663 970 9.784531 AAAGTAGTACAACTATCTATACGGCTA 57.215 33.333 2.52 0.00 32.65 3.93
664 971 8.688747 AAAGTAGTACAACTATCTATACGGCT 57.311 34.615 2.52 0.00 32.65 5.52
665 972 9.741647 AAAAAGTAGTACAACTATCTATACGGC 57.258 33.333 2.52 0.00 32.65 5.68
681 989 7.733773 TGATCTCTGATGGGAAAAAGTAGTA 57.266 36.000 0.00 0.00 0.00 1.82
723 1035 3.506067 GCCAAGGCTTAAACTTTCTAGCA 59.494 43.478 0.00 0.00 38.26 3.49
794 1109 2.804527 TCAGCGCATCTTATCTCAATGC 59.195 45.455 11.47 0.00 41.82 3.56
830 1145 0.393077 AGACCACCAAACAGGACGAG 59.607 55.000 0.00 0.00 41.22 4.18
1233 3855 3.302365 AAACAAAGATTCCACGGCATG 57.698 42.857 0.00 0.00 0.00 4.06
1606 4265 1.343789 CGATGGAGTCCATGCTCATCT 59.656 52.381 29.60 2.95 45.26 2.90
1988 4718 2.204136 ACCTCCAGCACCATCCCA 60.204 61.111 0.00 0.00 0.00 4.37
2131 4864 0.738762 CCATGGCTGTCACTCACTCG 60.739 60.000 0.00 0.00 0.00 4.18
2167 4901 4.685169 AGTCATTACGCTTGTTTGGATG 57.315 40.909 0.00 0.00 0.00 3.51
2169 4903 4.890088 AGTAGTCATTACGCTTGTTTGGA 58.110 39.130 0.00 0.00 37.35 3.53
2170 4904 4.092968 GGAGTAGTCATTACGCTTGTTTGG 59.907 45.833 0.00 0.00 37.35 3.28
2171 4905 4.092968 GGGAGTAGTCATTACGCTTGTTTG 59.907 45.833 0.00 0.00 37.35 2.93
2173 4907 3.514309 AGGGAGTAGTCATTACGCTTGTT 59.486 43.478 0.00 0.00 37.35 2.83
2174 4908 3.097614 AGGGAGTAGTCATTACGCTTGT 58.902 45.455 0.00 0.00 37.35 3.16
2183 4928 2.508716 TCGGTACAGAGGGAGTAGTCAT 59.491 50.000 0.00 0.00 0.00 3.06
2187 4932 4.885907 TGTATTTCGGTACAGAGGGAGTAG 59.114 45.833 0.00 0.00 31.33 2.57
2188 4933 4.858850 TGTATTTCGGTACAGAGGGAGTA 58.141 43.478 0.00 0.00 31.33 2.59
2189 4934 3.705051 TGTATTTCGGTACAGAGGGAGT 58.295 45.455 0.00 0.00 31.33 3.85
2190 4935 4.099573 ACATGTATTTCGGTACAGAGGGAG 59.900 45.833 0.00 0.00 37.93 4.30
2191 4936 4.028131 ACATGTATTTCGGTACAGAGGGA 58.972 43.478 0.00 0.00 37.93 4.20
2192 4937 4.369182 GACATGTATTTCGGTACAGAGGG 58.631 47.826 0.00 0.00 37.93 4.30
2193 4938 4.042398 CGACATGTATTTCGGTACAGAGG 58.958 47.826 0.00 0.00 37.93 3.69
2194 4939 3.486108 GCGACATGTATTTCGGTACAGAG 59.514 47.826 0.00 0.00 37.93 3.35
2195 4940 3.129813 AGCGACATGTATTTCGGTACAGA 59.870 43.478 7.49 0.00 43.71 3.41
2196 4941 3.242944 CAGCGACATGTATTTCGGTACAG 59.757 47.826 8.74 0.00 43.70 2.74
2197 4942 3.183754 CAGCGACATGTATTTCGGTACA 58.816 45.455 8.74 0.00 43.70 2.90
2198 4943 2.538449 CCAGCGACATGTATTTCGGTAC 59.462 50.000 8.74 0.00 43.70 3.34
2199 4944 2.427812 TCCAGCGACATGTATTTCGGTA 59.572 45.455 8.74 0.00 43.70 4.02
2200 4945 1.206132 TCCAGCGACATGTATTTCGGT 59.794 47.619 0.00 0.07 46.29 4.69
2201 4946 1.860950 CTCCAGCGACATGTATTTCGG 59.139 52.381 0.00 0.00 35.73 4.30
2202 4947 2.540515 ACTCCAGCGACATGTATTTCG 58.459 47.619 0.00 0.00 38.31 3.46
2203 4948 3.491267 GCTACTCCAGCGACATGTATTTC 59.509 47.826 0.00 0.00 41.37 2.17
2204 4949 3.458189 GCTACTCCAGCGACATGTATTT 58.542 45.455 0.00 0.00 41.37 1.40
2205 4950 3.099267 GCTACTCCAGCGACATGTATT 57.901 47.619 0.00 0.00 41.37 1.89
2206 4951 2.802787 GCTACTCCAGCGACATGTAT 57.197 50.000 0.00 0.00 41.37 2.29
2216 4961 2.114616 ACTCCCAATCAGCTACTCCAG 58.885 52.381 0.00 0.00 0.00 3.86
2217 4962 2.254152 ACTCCCAATCAGCTACTCCA 57.746 50.000 0.00 0.00 0.00 3.86
2218 4963 3.301274 ACTACTCCCAATCAGCTACTCC 58.699 50.000 0.00 0.00 0.00 3.85
2219 4964 4.278919 GGTACTACTCCCAATCAGCTACTC 59.721 50.000 0.00 0.00 0.00 2.59
2220 4965 4.216708 GGTACTACTCCCAATCAGCTACT 58.783 47.826 0.00 0.00 0.00 2.57
2221 4966 3.321396 GGGTACTACTCCCAATCAGCTAC 59.679 52.174 0.00 0.00 44.05 3.58
2222 4967 3.573695 GGGTACTACTCCCAATCAGCTA 58.426 50.000 0.00 0.00 44.05 3.32
2223 4968 2.399580 GGGTACTACTCCCAATCAGCT 58.600 52.381 0.00 0.00 44.05 4.24
2224 4969 2.912690 GGGTACTACTCCCAATCAGC 57.087 55.000 0.00 0.00 44.05 4.26
2231 4976 2.699321 GTGGAAGATGGGTACTACTCCC 59.301 54.545 0.00 0.00 44.81 4.30
2232 4977 3.371965 TGTGGAAGATGGGTACTACTCC 58.628 50.000 0.00 0.00 0.00 3.85
2233 4978 3.181474 GCTGTGGAAGATGGGTACTACTC 60.181 52.174 0.00 0.00 0.00 2.59
2234 4979 2.766828 GCTGTGGAAGATGGGTACTACT 59.233 50.000 0.00 0.00 0.00 2.57
2235 4980 2.500098 TGCTGTGGAAGATGGGTACTAC 59.500 50.000 0.00 0.00 0.00 2.73
2236 4981 2.827755 TGCTGTGGAAGATGGGTACTA 58.172 47.619 0.00 0.00 0.00 1.82
2237 4982 1.656587 TGCTGTGGAAGATGGGTACT 58.343 50.000 0.00 0.00 0.00 2.73
2273 5018 3.920446 GTGCCCACGTCCATTAATTTTT 58.080 40.909 0.00 0.00 0.00 1.94
2297 5042 5.529430 TCACAATTATACATTGCCCTAACGG 59.471 40.000 7.25 0.00 32.55 4.44
2298 5043 6.037720 TGTCACAATTATACATTGCCCTAACG 59.962 38.462 7.25 0.00 32.55 3.18
2299 5044 7.328277 TGTCACAATTATACATTGCCCTAAC 57.672 36.000 7.25 0.00 32.55 2.34
2330 5075 8.874156 TCTTAGCATTTATCCTATGTGTCATCT 58.126 33.333 0.00 0.00 0.00 2.90
2332 5077 9.445878 CATCTTAGCATTTATCCTATGTGTCAT 57.554 33.333 0.00 0.00 0.00 3.06
2334 5079 8.097038 TCCATCTTAGCATTTATCCTATGTGTC 58.903 37.037 0.00 0.00 0.00 3.67
2335 5080 7.977818 TCCATCTTAGCATTTATCCTATGTGT 58.022 34.615 0.00 0.00 0.00 3.72
2393 5138 8.320617 GCTAAGGAATCATCTCTCAAATAGGAT 58.679 37.037 0.00 0.00 0.00 3.24
2402 5148 7.877097 ACATGTTATGCTAAGGAATCATCTCTC 59.123 37.037 0.00 0.00 0.00 3.20
2413 5159 6.701841 ACGTGATTAGACATGTTATGCTAAGG 59.298 38.462 0.00 0.00 36.76 2.69
2470 5216 9.267071 ACAAGCCTAAAATGGGTTATCTTTTAT 57.733 29.630 0.00 0.00 44.87 1.40
2474 5220 7.410991 AGTACAAGCCTAAAATGGGTTATCTT 58.589 34.615 0.00 0.00 44.87 2.40
2503 5249 8.562052 GCATGTAATTCAGATATGACAATGACA 58.438 33.333 0.00 0.00 0.00 3.58
2504 5250 8.562052 TGCATGTAATTCAGATATGACAATGAC 58.438 33.333 0.00 0.00 0.00 3.06
2505 5251 8.680039 TGCATGTAATTCAGATATGACAATGA 57.320 30.769 0.00 0.00 0.00 2.57
2506 5252 9.394477 CTTGCATGTAATTCAGATATGACAATG 57.606 33.333 0.00 0.00 0.00 2.82
2571 5317 5.366477 TGCACCCACATATCAAGATCTAAGA 59.634 40.000 0.00 0.00 0.00 2.10
2628 5375 5.863397 CCGTGAATGTAGCATTGTTGAAAAT 59.137 36.000 0.00 0.00 0.00 1.82
2651 5398 2.125773 TCCGTGAAGAGTACTCCTCC 57.874 55.000 19.38 9.22 41.47 4.30
2652 5399 5.125097 TGTTATTCCGTGAAGAGTACTCCTC 59.875 44.000 19.38 16.34 40.80 3.71
2653 5400 5.014858 TGTTATTCCGTGAAGAGTACTCCT 58.985 41.667 19.38 6.46 0.00 3.69
2654 5401 5.100943 GTGTTATTCCGTGAAGAGTACTCC 58.899 45.833 19.38 5.74 0.00 3.85
2655 5402 5.100943 GGTGTTATTCCGTGAAGAGTACTC 58.899 45.833 15.41 15.41 0.00 2.59
2656 5403 4.525487 TGGTGTTATTCCGTGAAGAGTACT 59.475 41.667 0.00 0.00 0.00 2.73
2657 5404 4.813027 TGGTGTTATTCCGTGAAGAGTAC 58.187 43.478 0.00 0.00 0.00 2.73
2658 5405 4.081862 CCTGGTGTTATTCCGTGAAGAGTA 60.082 45.833 0.00 0.00 0.00 2.59
2659 5406 3.306780 CCTGGTGTTATTCCGTGAAGAGT 60.307 47.826 0.00 0.00 0.00 3.24
2660 5407 3.262420 CCTGGTGTTATTCCGTGAAGAG 58.738 50.000 0.00 0.00 0.00 2.85
2661 5408 2.027561 CCCTGGTGTTATTCCGTGAAGA 60.028 50.000 0.00 0.00 0.00 2.87
2662 5409 2.290071 ACCCTGGTGTTATTCCGTGAAG 60.290 50.000 0.00 0.00 0.00 3.02
2678 5425 6.262273 AGTCACAAACACTATGTAAAACCCTG 59.738 38.462 0.00 0.00 0.00 4.45
2679 5426 6.362248 AGTCACAAACACTATGTAAAACCCT 58.638 36.000 0.00 0.00 0.00 4.34
2689 5437 6.354130 ACACCTAACAAGTCACAAACACTAT 58.646 36.000 0.00 0.00 0.00 2.12
2713 5461 5.367937 CCTCTCTCTCCCTTAATCCAATCAA 59.632 44.000 0.00 0.00 0.00 2.57
2740 5488 1.548719 GTAATTTTCAGGTGGGTGGGC 59.451 52.381 0.00 0.00 0.00 5.36
2758 5506 4.355549 TCTAATTCTCTTCAACCCCCGTA 58.644 43.478 0.00 0.00 0.00 4.02
2760 5508 3.906720 TCTAATTCTCTTCAACCCCCG 57.093 47.619 0.00 0.00 0.00 5.73
2761 5509 5.437191 TCTTCTAATTCTCTTCAACCCCC 57.563 43.478 0.00 0.00 0.00 5.40
2802 5553 4.362279 TGCTAAACGTACGGGCTTATTAG 58.638 43.478 21.06 16.32 0.00 1.73
2877 5632 5.591067 ACGAGTTCAAGGTTTATTTTGGACA 59.409 36.000 0.00 0.00 35.65 4.02
2904 5659 0.165295 GCGTTCGGTTTAGCCTTCAC 59.835 55.000 0.00 0.00 34.25 3.18
2905 5660 0.249953 TGCGTTCGGTTTAGCCTTCA 60.250 50.000 0.00 0.00 34.25 3.02
2916 5671 4.334481 AGGGATTAAAACTTATGCGTTCGG 59.666 41.667 0.00 0.00 0.00 4.30
2925 5680 7.450014 TGTGCTGATTTCAGGGATTAAAACTTA 59.550 33.333 9.49 0.00 43.94 2.24
2932 5687 3.010027 TGGTGTGCTGATTTCAGGGATTA 59.990 43.478 9.49 0.00 43.94 1.75
2986 5741 0.625849 ATCCCGTTGAGAATGCCCTT 59.374 50.000 0.00 0.00 0.00 3.95
2989 5744 1.463674 ACAATCCCGTTGAGAATGCC 58.536 50.000 0.00 0.00 40.37 4.40
3086 5842 7.452630 TTTTTGGTATTTTTAAGTGTCACGC 57.547 32.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.