Multiple sequence alignment - TraesCS6D01G137400

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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 TraesCS6D01G137400 chr6D 100.000 2707 0 0 1 2707 106047847 106050553 0.000000e+00 5000.0
1 TraesCS6D01G137400 chr6D 97.917 96 2 0 692 787 135462280 135462185 1.670000e-37 167.0
2 TraesCS6D01G137400 chr6D 97.917 96 2 0 692 787 145355476 145355381 1.670000e-37 167.0
3 TraesCS6D01G137400 chr6D 97.917 96 2 0 692 787 168257091 168257186 1.670000e-37 167.0
4 TraesCS6D01G137400 chr6A 91.994 1299 68 14 785 2052 129316784 129318077 0.000000e+00 1790.0
5 TraesCS6D01G137400 chr6A 89.101 367 24 7 289 640 129316400 129316765 2.470000e-120 442.0
6 TraesCS6D01G137400 chr6A 97.297 37 0 1 652 688 129316750 129316785 8.090000e-06 62.1
7 TraesCS6D01G137400 chr6B 90.171 1231 67 20 795 2008 192737977 192739170 0.000000e+00 1554.0
8 TraesCS6D01G137400 chr6B 94.299 421 9 11 2290 2706 192837983 192838392 4.920000e-177 630.0
9 TraesCS6D01G137400 chr6B 91.611 298 13 4 2004 2290 192837654 192837950 4.200000e-108 401.0
10 TraesCS6D01G137400 chr6B 84.840 343 26 15 364 690 192737496 192737828 3.360000e-84 322.0
11 TraesCS6D01G137400 chr5D 84.010 394 41 14 1236 1609 373763306 373763697 2.560000e-95 359.0
12 TraesCS6D01G137400 chr5D 86.038 265 29 5 845 1106 373762939 373763198 7.380000e-71 278.0
13 TraesCS6D01G137400 chr5D 85.455 55 5 2 1646 1700 373763750 373763801 1.000000e-03 54.7
14 TraesCS6D01G137400 chr5B 91.964 224 18 0 1236 1459 445174018 445174241 5.630000e-82 315.0
15 TraesCS6D01G137400 chr5B 84.151 265 30 6 845 1106 445173655 445173910 2.080000e-61 246.0
16 TraesCS6D01G137400 chr5B 93.827 81 5 0 1529 1609 445176983 445177063 3.660000e-24 122.0
17 TraesCS6D01G137400 chr5B 94.286 35 2 0 1666 1700 445177123 445177157 1.000000e-03 54.7
18 TraesCS6D01G137400 chr1B 78.663 389 55 23 1237 1612 428801993 428802366 1.620000e-57 233.0
19 TraesCS6D01G137400 chr1D 88.957 163 16 2 83 243 427826920 427827082 1.640000e-47 200.0
20 TraesCS6D01G137400 chr1D 88.060 67 8 0 1538 1604 316679100 316679166 2.230000e-11 80.5
21 TraesCS6D01G137400 chr3D 87.356 174 18 4 82 252 410670226 410670054 2.130000e-46 196.0
22 TraesCS6D01G137400 chr3D 88.024 167 17 3 84 247 238999575 238999409 7.650000e-46 195.0
23 TraesCS6D01G137400 chr3D 87.425 167 19 2 81 245 571465531 571465365 9.890000e-45 191.0
24 TraesCS6D01G137400 chr3D 87.425 167 19 2 81 245 579494789 579494955 9.890000e-45 191.0
25 TraesCS6D01G137400 chr3D 97.917 96 2 0 692 787 213393626 213393531 1.670000e-37 167.0
26 TraesCS6D01G137400 chr1A 87.952 166 18 2 81 244 15539994 15540159 7.650000e-46 195.0
27 TraesCS6D01G137400 chr1A 97.917 96 2 0 692 787 3079827 3079922 1.670000e-37 167.0
28 TraesCS6D01G137400 chr1A 97.917 96 2 0 692 787 554514413 554514508 1.670000e-37 167.0
29 TraesCS6D01G137400 chr1A 87.857 140 13 1 971 1106 397769737 397769876 7.760000e-36 161.0
30 TraesCS6D01G137400 chr4D 87.135 171 19 3 76 244 230542718 230542549 9.890000e-45 191.0
31 TraesCS6D01G137400 chr4D 86.705 173 19 4 74 244 58643748 58643918 3.560000e-44 189.0
32 TraesCS6D01G137400 chr4D 95.455 110 5 0 997 1106 373933838 373933729 2.770000e-40 176.0
33 TraesCS6D01G137400 chr3B 87.500 168 17 4 79 244 107637927 107637762 9.890000e-45 191.0
34 TraesCS6D01G137400 chr4B 91.176 136 12 0 1232 1367 5466296 5466431 4.600000e-43 185.0
35 TraesCS6D01G137400 chr4B 93.860 114 7 0 993 1106 459947255 459947142 3.580000e-39 172.0
36 TraesCS6D01G137400 chr4A 91.667 132 11 0 1236 1367 601060003 601060134 1.660000e-42 183.0
37 TraesCS6D01G137400 chr4A 95.455 110 5 0 997 1106 90518910 90519019 2.770000e-40 176.0
38 TraesCS6D01G137400 chr4A 93.860 114 7 0 993 1106 90591195 90591308 3.580000e-39 172.0
39 TraesCS6D01G137400 chr4A 98.958 96 1 0 692 787 310740762 310740857 3.580000e-39 172.0
40 TraesCS6D01G137400 chrUn 97.917 96 2 0 692 787 216516438 216516343 1.670000e-37 167.0
41 TraesCS6D01G137400 chrUn 97.917 96 2 0 692 787 286266945 286267040 1.670000e-37 167.0
42 TraesCS6D01G137400 chr2B 88.889 135 15 0 1240 1374 677856465 677856331 1.670000e-37 167.0
43 TraesCS6D01G137400 chr2B 88.333 120 14 0 1238 1357 678199599 678199480 7.810000e-31 145.0
44 TraesCS6D01G137400 chr2B 89.610 77 7 1 1531 1606 678068665 678068589 2.220000e-16 97.1
45 TraesCS6D01G137400 chr2B 91.304 69 6 0 1538 1606 678088503 678088435 7.980000e-16 95.3
46 TraesCS6D01G137400 chr2B 88.462 78 8 1 1531 1607 678198052 678197975 2.870000e-15 93.5
47 TraesCS6D01G137400 chr2D 89.231 130 14 0 1240 1369 565484743 565484614 2.160000e-36 163.0
48 TraesCS6D01G137400 chr2D 89.744 78 7 1 1531 1607 565860997 565860920 6.170000e-17 99.0
49 TraesCS6D01G137400 chr2D 90.411 73 7 0 1534 1606 565590577 565590505 2.220000e-16 97.1
50 TraesCS6D01G137400 chr2D 90.541 74 6 1 1531 1603 642783387 642783460 2.220000e-16 97.1
51 TraesCS6D01G137400 chr2D 90.909 66 6 0 1538 1603 43952540 43952605 3.710000e-14 89.8
52 TraesCS6D01G137400 chr2D 89.855 69 7 0 1535 1603 43964537 43964605 3.710000e-14 89.8
53 TraesCS6D01G137400 chr2A 89.744 78 7 1 1531 1607 706200537 706200460 6.170000e-17 99.0
54 TraesCS6D01G137400 chr7D 87.324 71 9 0 1537 1607 586766115 586766185 6.210000e-12 82.4
55 TraesCS6D01G137400 chr7D 87.324 71 9 0 1537 1607 586783979 586784049 6.210000e-12 82.4
56 TraesCS6D01G137400 chr5A 100.000 28 0 0 1673 1700 475614708 475614735 5.000000e-03 52.8


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 TraesCS6D01G137400 chr6D 106047847 106050553 2706 False 5000.000000 5000 100.000000 1 2707 1 chr6D.!!$F1 2706
1 TraesCS6D01G137400 chr6A 129316400 129318077 1677 False 764.700000 1790 92.797333 289 2052 3 chr6A.!!$F1 1763
2 TraesCS6D01G137400 chr6B 192737496 192739170 1674 False 938.000000 1554 87.505500 364 2008 2 chr6B.!!$F1 1644
3 TraesCS6D01G137400 chr6B 192837654 192838392 738 False 515.500000 630 92.955000 2004 2706 2 chr6B.!!$F2 702
4 TraesCS6D01G137400 chr5D 373762939 373763801 862 False 230.566667 359 85.167667 845 1700 3 chr5D.!!$F1 855

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
266 267 0.037139 TTATGCCGTACCGTGTGCTT 60.037 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2357 0.108585 TCCAACTGTTCCTGGTCAGC 59.891 55.0 16.74 0.0 35.37 4.26 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
26 27 3.197790 CGCGTGCATCCCCTTCTG 61.198 66.667 0.00 0.00 0.00 3.02
27 28 3.512516 GCGTGCATCCCCTTCTGC 61.513 66.667 0.00 0.00 38.87 4.26
28 29 2.825836 CGTGCATCCCCTTCTGCC 60.826 66.667 0.00 0.00 37.59 4.85
29 30 2.440980 GTGCATCCCCTTCTGCCC 60.441 66.667 0.00 0.00 37.59 5.36
30 31 3.743017 TGCATCCCCTTCTGCCCC 61.743 66.667 0.00 0.00 37.59 5.80
31 32 4.529731 GCATCCCCTTCTGCCCCC 62.530 72.222 0.00 0.00 32.15 5.40
32 33 2.697644 CATCCCCTTCTGCCCCCT 60.698 66.667 0.00 0.00 0.00 4.79
33 34 2.130576 ATCCCCTTCTGCCCCCTT 59.869 61.111 0.00 0.00 0.00 3.95
34 35 2.009302 ATCCCCTTCTGCCCCCTTC 61.009 63.158 0.00 0.00 0.00 3.46
35 36 3.744155 CCCCTTCTGCCCCCTTCC 61.744 72.222 0.00 0.00 0.00 3.46
36 37 3.744155 CCCTTCTGCCCCCTTCCC 61.744 72.222 0.00 0.00 0.00 3.97
37 38 3.744155 CCTTCTGCCCCCTTCCCC 61.744 72.222 0.00 0.00 0.00 4.81
38 39 3.744155 CTTCTGCCCCCTTCCCCC 61.744 72.222 0.00 0.00 0.00 5.40
39 40 4.301662 TTCTGCCCCCTTCCCCCT 62.302 66.667 0.00 0.00 0.00 4.79
40 41 4.760220 TCTGCCCCCTTCCCCCTC 62.760 72.222 0.00 0.00 0.00 4.30
44 45 2.204464 CCCCCTTCCCCCTCCTTT 60.204 66.667 0.00 0.00 0.00 3.11
45 46 1.862138 CCCCCTTCCCCCTCCTTTT 60.862 63.158 0.00 0.00 0.00 2.27
46 47 1.452226 CCCCCTTCCCCCTCCTTTTT 61.452 60.000 0.00 0.00 0.00 1.94
47 48 0.252239 CCCCTTCCCCCTCCTTTTTG 60.252 60.000 0.00 0.00 0.00 2.44
48 49 0.904865 CCCTTCCCCCTCCTTTTTGC 60.905 60.000 0.00 0.00 0.00 3.68
49 50 1.250840 CCTTCCCCCTCCTTTTTGCG 61.251 60.000 0.00 0.00 0.00 4.85
50 51 0.539669 CTTCCCCCTCCTTTTTGCGT 60.540 55.000 0.00 0.00 0.00 5.24
51 52 0.825840 TTCCCCCTCCTTTTTGCGTG 60.826 55.000 0.00 0.00 0.00 5.34
52 53 1.530655 CCCCCTCCTTTTTGCGTGT 60.531 57.895 0.00 0.00 0.00 4.49
53 54 1.524008 CCCCCTCCTTTTTGCGTGTC 61.524 60.000 0.00 0.00 0.00 3.67
54 55 1.574428 CCCTCCTTTTTGCGTGTCG 59.426 57.895 0.00 0.00 0.00 4.35
55 56 1.164041 CCCTCCTTTTTGCGTGTCGT 61.164 55.000 0.00 0.00 0.00 4.34
56 57 0.041312 CCTCCTTTTTGCGTGTCGTG 60.041 55.000 0.00 0.00 0.00 4.35
57 58 0.934496 CTCCTTTTTGCGTGTCGTGA 59.066 50.000 0.00 0.00 0.00 4.35
58 59 0.653636 TCCTTTTTGCGTGTCGTGAC 59.346 50.000 0.00 0.00 0.00 3.67
59 60 0.655733 CCTTTTTGCGTGTCGTGACT 59.344 50.000 1.23 0.00 0.00 3.41
60 61 1.594518 CCTTTTTGCGTGTCGTGACTG 60.595 52.381 1.23 0.00 0.00 3.51
61 62 0.375454 TTTTTGCGTGTCGTGACTGG 59.625 50.000 1.23 0.00 0.00 4.00
62 63 0.741574 TTTTGCGTGTCGTGACTGGT 60.742 50.000 1.23 0.00 0.00 4.00
63 64 0.102663 TTTGCGTGTCGTGACTGGTA 59.897 50.000 1.23 0.00 0.00 3.25
64 65 0.102663 TTGCGTGTCGTGACTGGTAA 59.897 50.000 1.23 0.00 0.00 2.85
65 66 0.102663 TGCGTGTCGTGACTGGTAAA 59.897 50.000 1.23 0.00 0.00 2.01
66 67 1.269883 TGCGTGTCGTGACTGGTAAAT 60.270 47.619 1.23 0.00 0.00 1.40
67 68 2.030096 TGCGTGTCGTGACTGGTAAATA 60.030 45.455 1.23 0.00 0.00 1.40
68 69 3.184541 GCGTGTCGTGACTGGTAAATAT 58.815 45.455 1.23 0.00 0.00 1.28
69 70 4.142425 TGCGTGTCGTGACTGGTAAATATA 60.142 41.667 1.23 0.00 0.00 0.86
70 71 4.980434 GCGTGTCGTGACTGGTAAATATAT 59.020 41.667 1.23 0.00 0.00 0.86
71 72 6.144854 GCGTGTCGTGACTGGTAAATATATA 58.855 40.000 1.23 0.00 0.00 0.86
72 73 6.087291 GCGTGTCGTGACTGGTAAATATATAC 59.913 42.308 1.23 0.00 0.00 1.47
73 74 6.301607 CGTGTCGTGACTGGTAAATATATACG 59.698 42.308 1.23 0.00 0.00 3.06
74 75 6.087291 GTGTCGTGACTGGTAAATATATACGC 59.913 42.308 1.23 0.00 0.00 4.42
75 76 6.144854 GTCGTGACTGGTAAATATATACGCA 58.855 40.000 0.00 0.00 0.00 5.24
76 77 6.805271 GTCGTGACTGGTAAATATATACGCAT 59.195 38.462 0.00 0.00 0.00 4.73
77 78 7.964559 GTCGTGACTGGTAAATATATACGCATA 59.035 37.037 0.00 0.00 0.00 3.14
78 79 8.513774 TCGTGACTGGTAAATATATACGCATAA 58.486 33.333 0.00 0.00 0.00 1.90
79 80 9.131416 CGTGACTGGTAAATATATACGCATAAA 57.869 33.333 0.00 0.00 0.00 1.40
93 94 4.868067 ACGCATAAATACTACTCCCTTCG 58.132 43.478 0.00 0.00 0.00 3.79
94 95 4.340381 ACGCATAAATACTACTCCCTTCGT 59.660 41.667 0.00 0.00 0.00 3.85
95 96 5.163478 ACGCATAAATACTACTCCCTTCGTT 60.163 40.000 0.00 0.00 0.00 3.85
96 97 5.751990 CGCATAAATACTACTCCCTTCGTTT 59.248 40.000 0.00 0.00 0.00 3.60
97 98 6.074463 CGCATAAATACTACTCCCTTCGTTTC 60.074 42.308 0.00 0.00 0.00 2.78
98 99 6.985059 GCATAAATACTACTCCCTTCGTTTCT 59.015 38.462 0.00 0.00 0.00 2.52
99 100 8.139989 GCATAAATACTACTCCCTTCGTTTCTA 58.860 37.037 0.00 0.00 0.00 2.10
140 141 7.925043 AGATTCCACTATAGACTACATACGG 57.075 40.000 6.78 0.00 0.00 4.02
141 142 7.687388 AGATTCCACTATAGACTACATACGGA 58.313 38.462 6.78 0.00 0.00 4.69
142 143 7.825270 AGATTCCACTATAGACTACATACGGAG 59.175 40.741 6.78 0.00 0.00 4.63
143 144 5.243981 TCCACTATAGACTACATACGGAGC 58.756 45.833 6.78 0.00 0.00 4.70
144 145 5.001874 CCACTATAGACTACATACGGAGCA 58.998 45.833 6.78 0.00 0.00 4.26
145 146 5.472478 CCACTATAGACTACATACGGAGCAA 59.528 44.000 6.78 0.00 0.00 3.91
146 147 6.016527 CCACTATAGACTACATACGGAGCAAA 60.017 42.308 6.78 0.00 0.00 3.68
147 148 7.423199 CACTATAGACTACATACGGAGCAAAA 58.577 38.462 6.78 0.00 0.00 2.44
148 149 8.082852 CACTATAGACTACATACGGAGCAAAAT 58.917 37.037 6.78 0.00 0.00 1.82
149 150 8.082852 ACTATAGACTACATACGGAGCAAAATG 58.917 37.037 6.78 0.00 0.00 2.32
150 151 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
151 152 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
152 153 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
153 154 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
154 155 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
155 156 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
156 157 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
157 158 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
158 159 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
159 160 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
160 161 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
161 162 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
162 163 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
175 176 8.206325 AGTGAATCTACACTCTAAAATGCATG 57.794 34.615 0.00 0.00 46.36 4.06
176 177 7.826252 AGTGAATCTACACTCTAAAATGCATGT 59.174 33.333 0.00 0.00 46.36 3.21
177 178 9.098355 GTGAATCTACACTCTAAAATGCATGTA 57.902 33.333 0.00 0.00 37.73 2.29
178 179 9.098355 TGAATCTACACTCTAAAATGCATGTAC 57.902 33.333 0.00 0.00 0.00 2.90
179 180 9.098355 GAATCTACACTCTAAAATGCATGTACA 57.902 33.333 0.00 0.00 0.00 2.90
180 181 9.618890 AATCTACACTCTAAAATGCATGTACAT 57.381 29.630 1.41 1.41 0.00 2.29
182 183 9.529325 TCTACACTCTAAAATGCATGTACATAC 57.471 33.333 8.32 3.18 0.00 2.39
183 184 9.313118 CTACACTCTAAAATGCATGTACATACA 57.687 33.333 11.15 11.15 40.98 2.29
185 186 9.177608 ACACTCTAAAATGCATGTACATACATT 57.822 29.630 23.13 23.13 43.99 2.71
186 187 9.655769 CACTCTAAAATGCATGTACATACATTC 57.344 33.333 26.96 8.80 43.99 2.67
187 188 8.551205 ACTCTAAAATGCATGTACATACATTCG 58.449 33.333 26.96 19.69 43.99 3.34
188 189 8.432110 TCTAAAATGCATGTACATACATTCGT 57.568 30.769 26.96 21.15 43.99 3.85
189 190 9.535878 TCTAAAATGCATGTACATACATTCGTA 57.464 29.630 26.96 21.14 43.99 3.43
190 191 9.580916 CTAAAATGCATGTACATACATTCGTAC 57.419 33.333 26.96 4.20 43.99 3.67
191 192 5.822584 ATGCATGTACATACATTCGTACG 57.177 39.130 14.69 9.53 43.99 3.67
192 193 4.674475 TGCATGTACATACATTCGTACGT 58.326 39.130 16.05 0.00 43.99 3.57
197 198 7.997107 ATGTACATACATTCGTACGTGATTT 57.003 32.000 16.05 6.71 43.99 2.17
199 200 9.687210 ATGTACATACATTCGTACGTGATTTAT 57.313 29.630 16.05 10.35 43.99 1.40
203 204 9.177304 ACATACATTCGTACGTGATTTATAGTG 57.823 33.333 16.05 2.86 0.00 2.74
204 205 9.389570 CATACATTCGTACGTGATTTATAGTGA 57.610 33.333 16.05 0.00 0.00 3.41
205 206 9.955208 ATACATTCGTACGTGATTTATAGTGAA 57.045 29.630 16.05 0.00 0.00 3.18
206 207 8.692110 ACATTCGTACGTGATTTATAGTGAAA 57.308 30.769 16.05 0.00 0.00 2.69
207 208 9.309516 ACATTCGTACGTGATTTATAGTGAAAT 57.690 29.630 16.05 0.00 0.00 2.17
208 209 9.779237 CATTCGTACGTGATTTATAGTGAAATC 57.221 33.333 16.05 2.60 43.33 2.17
209 210 9.745880 ATTCGTACGTGATTTATAGTGAAATCT 57.254 29.630 16.05 0.00 43.40 2.40
210 211 9.577110 TTCGTACGTGATTTATAGTGAAATCTT 57.423 29.630 16.05 0.00 43.40 2.40
211 212 9.577110 TCGTACGTGATTTATAGTGAAATCTTT 57.423 29.630 16.05 0.00 43.40 2.52
259 260 4.552355 TGAGTATTCATTATGCCGTACCG 58.448 43.478 0.00 0.00 0.00 4.02
260 261 4.038282 TGAGTATTCATTATGCCGTACCGT 59.962 41.667 0.00 0.00 0.00 4.83
261 262 4.304110 AGTATTCATTATGCCGTACCGTG 58.696 43.478 0.00 0.00 0.00 4.94
262 263 2.676632 TTCATTATGCCGTACCGTGT 57.323 45.000 0.00 0.00 0.00 4.49
263 264 1.929230 TCATTATGCCGTACCGTGTG 58.071 50.000 0.00 0.00 0.00 3.82
264 265 0.303493 CATTATGCCGTACCGTGTGC 59.697 55.000 0.00 0.00 0.00 4.57
265 266 0.177141 ATTATGCCGTACCGTGTGCT 59.823 50.000 0.00 0.00 0.00 4.40
266 267 0.037139 TTATGCCGTACCGTGTGCTT 60.037 50.000 0.00 0.00 0.00 3.91
267 268 0.037139 TATGCCGTACCGTGTGCTTT 60.037 50.000 0.00 0.00 0.00 3.51
268 269 0.887387 ATGCCGTACCGTGTGCTTTT 60.887 50.000 0.00 0.00 0.00 2.27
269 270 1.096386 TGCCGTACCGTGTGCTTTTT 61.096 50.000 0.00 0.00 0.00 1.94
285 286 1.073098 TTTTTCTCTCCCACCCCTCC 58.927 55.000 0.00 0.00 0.00 4.30
286 287 0.196118 TTTTCTCTCCCACCCCTCCT 59.804 55.000 0.00 0.00 0.00 3.69
287 288 0.196118 TTTCTCTCCCACCCCTCCTT 59.804 55.000 0.00 0.00 0.00 3.36
324 325 1.510480 GCCTGGCTCACAGTGTTGTC 61.510 60.000 12.43 0.00 46.06 3.18
332 333 2.206750 TCACAGTGTTGTCTAAACGGC 58.793 47.619 0.00 0.00 34.62 5.68
333 334 1.263217 CACAGTGTTGTCTAAACGGCC 59.737 52.381 0.00 0.00 34.62 6.13
354 355 1.895798 CGGCCTGATTCAGCCTAGATA 59.104 52.381 18.68 0.00 0.00 1.98
476 486 4.276926 AGCTTTCTTCAATGACACCACTTC 59.723 41.667 0.00 0.00 0.00 3.01
478 488 5.561725 GCTTTCTTCAATGACACCACTTCTC 60.562 44.000 0.00 0.00 0.00 2.87
483 493 7.453393 TCTTCAATGACACCACTTCTCTAAAT 58.547 34.615 0.00 0.00 0.00 1.40
589 611 4.592485 TGTTGCGGTTGGAAATATTGTT 57.408 36.364 0.00 0.00 0.00 2.83
616 662 3.846955 GCAAATTGCATGAGGCCTT 57.153 47.368 13.73 0.00 44.26 4.35
624 670 6.543430 AATTGCATGAGGCCTTGTTAAATA 57.457 33.333 6.77 0.00 43.89 1.40
625 671 5.581126 TTGCATGAGGCCTTGTTAAATAG 57.419 39.130 6.77 0.00 43.89 1.73
626 672 4.854173 TGCATGAGGCCTTGTTAAATAGA 58.146 39.130 6.77 0.00 43.89 1.98
627 673 5.448654 TGCATGAGGCCTTGTTAAATAGAT 58.551 37.500 6.77 0.00 43.89 1.98
628 674 5.300034 TGCATGAGGCCTTGTTAAATAGATG 59.700 40.000 6.77 0.00 43.89 2.90
629 675 5.300286 GCATGAGGCCTTGTTAAATAGATGT 59.700 40.000 6.77 0.00 36.11 3.06
630 676 6.486657 GCATGAGGCCTTGTTAAATAGATGTA 59.513 38.462 6.77 0.00 36.11 2.29
631 677 7.520614 GCATGAGGCCTTGTTAAATAGATGTAC 60.521 40.741 6.77 0.00 36.11 2.90
632 678 6.354130 TGAGGCCTTGTTAAATAGATGTACC 58.646 40.000 6.77 0.00 0.00 3.34
633 679 5.365619 AGGCCTTGTTAAATAGATGTACCG 58.634 41.667 0.00 0.00 0.00 4.02
634 680 5.104652 AGGCCTTGTTAAATAGATGTACCGT 60.105 40.000 0.00 0.00 0.00 4.83
635 681 5.007332 GGCCTTGTTAAATAGATGTACCGTG 59.993 44.000 0.00 0.00 0.00 4.94
636 682 5.813672 GCCTTGTTAAATAGATGTACCGTGA 59.186 40.000 0.00 0.00 0.00 4.35
637 683 6.482308 GCCTTGTTAAATAGATGTACCGTGAT 59.518 38.462 0.00 0.00 0.00 3.06
638 684 7.012044 GCCTTGTTAAATAGATGTACCGTGATT 59.988 37.037 0.00 0.00 0.00 2.57
639 685 8.889717 CCTTGTTAAATAGATGTACCGTGATTT 58.110 33.333 0.00 0.00 0.00 2.17
640 686 9.916397 CTTGTTAAATAGATGTACCGTGATTTC 57.084 33.333 0.00 0.00 0.00 2.17
641 687 9.438228 TTGTTAAATAGATGTACCGTGATTTCA 57.562 29.630 0.00 0.00 0.00 2.69
642 688 8.875803 TGTTAAATAGATGTACCGTGATTTCAC 58.124 33.333 0.46 0.46 43.15 3.18
643 689 9.095065 GTTAAATAGATGTACCGTGATTTCACT 57.905 33.333 8.91 0.00 44.34 3.41
646 692 9.661563 AAATAGATGTACCGTGATTTCACTAAA 57.338 29.630 8.91 0.00 44.34 1.85
647 693 9.661563 AATAGATGTACCGTGATTTCACTAAAA 57.338 29.630 8.91 0.00 44.34 1.52
648 694 7.972832 AGATGTACCGTGATTTCACTAAAAA 57.027 32.000 8.91 0.00 44.34 1.94
683 729 7.147620 ACCGTGATTTATGGGAGTAGTTATCAA 60.148 37.037 0.00 0.00 39.98 2.57
685 731 7.385205 CGTGATTTATGGGAGTAGTTATCAAGG 59.615 40.741 0.00 0.00 0.00 3.61
688 734 9.847224 GATTTATGGGAGTAGTTATCAAGGAAA 57.153 33.333 0.00 0.00 0.00 3.13
689 735 9.628500 ATTTATGGGAGTAGTTATCAAGGAAAC 57.372 33.333 0.00 0.00 0.00 2.78
691 737 7.989947 ATGGGAGTAGTTATCAAGGAAACTA 57.010 36.000 0.00 0.00 42.68 2.24
693 739 7.792032 TGGGAGTAGTTATCAAGGAAACTATG 58.208 38.462 0.00 0.00 42.68 2.23
695 741 8.483758 GGGAGTAGTTATCAAGGAAACTATGAA 58.516 37.037 0.00 0.00 42.68 2.57
696 742 9.535878 GGAGTAGTTATCAAGGAAACTATGAAG 57.464 37.037 0.00 0.00 42.68 3.02
705 751 8.703604 TCAAGGAAACTATGAAGAGATTAACG 57.296 34.615 0.00 0.00 42.68 3.18
707 753 8.812329 CAAGGAAACTATGAAGAGATTAACGAG 58.188 37.037 0.00 0.00 42.68 4.18
709 755 8.192110 AGGAAACTATGAAGAGATTAACGAGAC 58.808 37.037 0.00 0.00 40.61 3.36
710 756 8.192110 GGAAACTATGAAGAGATTAACGAGACT 58.808 37.037 0.00 0.00 0.00 3.24
711 757 9.575783 GAAACTATGAAGAGATTAACGAGACTT 57.424 33.333 0.00 0.00 0.00 3.01
712 758 9.575783 AAACTATGAAGAGATTAACGAGACTTC 57.424 33.333 0.00 0.00 35.70 3.01
714 760 8.962679 ACTATGAAGAGATTAACGAGACTTCTT 58.037 33.333 0.00 0.00 36.00 2.52
718 764 8.024285 TGAAGAGATTAACGAGACTTCTTTCTC 58.976 37.037 0.00 0.00 39.01 2.87
720 766 8.117813 AGAGATTAACGAGACTTCTTTCTCTT 57.882 34.615 0.00 0.00 40.07 2.85
722 768 9.198837 GAGATTAACGAGACTTCTTTCTCTTTT 57.801 33.333 0.00 0.00 40.07 2.27
726 772 5.908341 ACGAGACTTCTTTCTCTTTTGAGT 58.092 37.500 0.00 0.00 46.30 3.41
731 777 9.497030 GAGACTTCTTTCTCTTTTGAGTTTTTC 57.503 33.333 0.00 0.00 46.30 2.29
732 778 9.237187 AGACTTCTTTCTCTTTTGAGTTTTTCT 57.763 29.630 0.00 0.00 46.30 2.52
733 779 9.283420 GACTTCTTTCTCTTTTGAGTTTTTCTG 57.717 33.333 0.00 0.00 46.30 3.02
734 780 8.246871 ACTTCTTTCTCTTTTGAGTTTTTCTGG 58.753 33.333 0.00 0.00 46.30 3.86
735 781 6.564328 TCTTTCTCTTTTGAGTTTTTCTGGC 58.436 36.000 0.00 0.00 46.30 4.85
737 783 3.315191 TCTCTTTTGAGTTTTTCTGGCGG 59.685 43.478 0.00 0.00 46.30 6.13
738 784 3.283751 TCTTTTGAGTTTTTCTGGCGGA 58.716 40.909 0.00 0.00 0.00 5.54
739 785 3.066203 TCTTTTGAGTTTTTCTGGCGGAC 59.934 43.478 0.00 0.00 0.00 4.79
742 788 0.875059 GAGTTTTTCTGGCGGACCTG 59.125 55.000 0.00 0.00 36.63 4.00
743 789 0.182775 AGTTTTTCTGGCGGACCTGT 59.817 50.000 0.00 0.00 36.34 4.00
744 790 0.591659 GTTTTTCTGGCGGACCTGTC 59.408 55.000 0.00 0.00 36.34 3.51
745 791 0.882927 TTTTTCTGGCGGACCTGTCG 60.883 55.000 0.00 0.00 36.34 4.35
752 798 4.717629 CGGACCTGTCGCGCAAGA 62.718 66.667 8.75 0.00 43.02 3.02
753 799 2.125512 GGACCTGTCGCGCAAGAT 60.126 61.111 8.75 0.00 43.02 2.40
754 800 2.167861 GGACCTGTCGCGCAAGATC 61.168 63.158 8.75 0.00 43.02 2.75
755 801 1.153745 GACCTGTCGCGCAAGATCT 60.154 57.895 8.75 0.00 43.02 2.75
756 802 0.737715 GACCTGTCGCGCAAGATCTT 60.738 55.000 8.75 0.88 43.02 2.40
759 805 0.095935 CTGTCGCGCAAGATCTTTGG 59.904 55.000 8.75 1.54 43.02 3.28
760 806 0.602638 TGTCGCGCAAGATCTTTGGT 60.603 50.000 8.75 0.00 43.02 3.67
761 807 0.095417 GTCGCGCAAGATCTTTGGTC 59.905 55.000 8.75 0.00 43.02 4.02
762 808 0.037326 TCGCGCAAGATCTTTGGTCT 60.037 50.000 8.75 0.00 43.02 3.85
763 809 0.798776 CGCGCAAGATCTTTGGTCTT 59.201 50.000 8.75 0.00 43.02 3.01
764 810 1.201965 CGCGCAAGATCTTTGGTCTTC 60.202 52.381 8.75 0.00 43.02 2.87
765 811 1.131315 GCGCAAGATCTTTGGTCTTCC 59.869 52.381 4.86 0.00 43.02 3.46
767 813 2.095461 GCAAGATCTTTGGTCTTCCCC 58.905 52.381 4.86 0.00 33.82 4.81
768 814 2.291217 GCAAGATCTTTGGTCTTCCCCT 60.291 50.000 4.86 0.00 33.82 4.79
769 815 3.350833 CAAGATCTTTGGTCTTCCCCTG 58.649 50.000 4.86 0.00 33.82 4.45
771 817 3.260205 AGATCTTTGGTCTTCCCCTGAA 58.740 45.455 0.00 0.00 0.00 3.02
772 818 3.657727 AGATCTTTGGTCTTCCCCTGAAA 59.342 43.478 0.00 0.00 0.00 2.69
774 820 2.158519 TCTTTGGTCTTCCCCTGAAACC 60.159 50.000 0.00 0.00 0.00 3.27
775 821 0.109723 TTGGTCTTCCCCTGAAACCG 59.890 55.000 0.00 0.00 32.50 4.44
777 823 0.618981 GGTCTTCCCCTGAAACCGAT 59.381 55.000 0.00 0.00 0.00 4.18
778 824 1.679032 GGTCTTCCCCTGAAACCGATG 60.679 57.143 0.00 0.00 0.00 3.84
779 825 1.278127 GTCTTCCCCTGAAACCGATGA 59.722 52.381 0.00 0.00 0.00 2.92
781 827 2.373836 TCTTCCCCTGAAACCGATGAAA 59.626 45.455 0.00 0.00 0.00 2.69
782 828 2.961531 TCCCCTGAAACCGATGAAAA 57.038 45.000 0.00 0.00 0.00 2.29
783 829 3.231207 TCCCCTGAAACCGATGAAAAA 57.769 42.857 0.00 0.00 0.00 1.94
843 932 9.961265 CTAACTAATTTGATGTGATCATGCATT 57.039 29.630 0.00 0.00 39.39 3.56
967 1063 1.705873 CGTATCCTACCTCTTGGGCT 58.294 55.000 0.00 0.00 39.10 5.19
968 1064 1.614413 CGTATCCTACCTCTTGGGCTC 59.386 57.143 0.00 0.00 39.10 4.70
976 1072 2.361230 TCTTGGGCTCGAGCGAGA 60.361 61.111 29.81 26.50 44.53 4.04
1156 1253 3.740128 GATCGATGTGCCGGCCACT 62.740 63.158 26.77 7.87 44.92 4.00
1191 1288 1.153784 CTCCGGCCGCGTTTACTAA 60.154 57.895 22.85 0.00 0.00 2.24
1212 1309 0.379316 TGCATATGCTTTGCGCTGAG 59.621 50.000 27.13 7.65 43.10 3.35
1491 1603 0.310543 TGCCGTGCAATTGAGTTCAC 59.689 50.000 10.34 6.74 34.76 3.18
1524 1640 5.664457 CCTATGACTGATTCTGTTGCTGTA 58.336 41.667 0.00 0.00 0.00 2.74
1622 1739 1.134580 ACGAGGTGAGCTAGCGTAGTA 60.135 52.381 9.55 0.00 32.94 1.82
1635 1752 9.279904 GAGCTAGCGTAGTATAATCAACTTATG 57.720 37.037 9.55 0.00 32.26 1.90
1636 1753 7.755822 AGCTAGCGTAGTATAATCAACTTATGC 59.244 37.037 9.55 0.00 33.86 3.14
1716 1852 0.859232 GTTTGTTTGAGCGAGCGAGA 59.141 50.000 0.00 0.00 0.00 4.04
1806 1943 0.109458 TAGCATCGTGTCCGTGTCAC 60.109 55.000 0.00 0.00 35.01 3.67
1860 2014 7.095899 GGTTTTAAGTTGAGTCGATCGTTAGTT 60.096 37.037 15.94 8.54 0.00 2.24
1876 2030 8.827177 ATCGTTAGTTTCATAGTCAAGTTCAA 57.173 30.769 0.00 0.00 0.00 2.69
2201 2365 3.877559 TGATAATGGAGTTGCTGACCAG 58.122 45.455 0.00 0.00 37.12 4.00
2226 2390 3.071892 ACAGTTGGACAGAACCCGAATAA 59.928 43.478 0.00 0.00 0.00 1.40
2248 2421 2.442413 CCCCCACACACAAATAACGAT 58.558 47.619 0.00 0.00 0.00 3.73
2293 2499 9.750125 GATACAAATTCTAAATGGGGAAACATC 57.250 33.333 0.00 0.00 0.00 3.06
2326 2532 8.577296 TGTCTAGTCGAGAAAATCCATATAAGG 58.423 37.037 0.00 0.00 35.37 2.69
2410 2616 9.517868 AATTTTCTTGCAAATGGATTAATTGGA 57.482 25.926 0.00 0.00 0.00 3.53
2411 2617 7.903995 TTTCTTGCAAATGGATTAATTGGAC 57.096 32.000 0.00 0.00 0.00 4.02
2412 2618 6.855763 TCTTGCAAATGGATTAATTGGACT 57.144 33.333 0.00 0.00 0.00 3.85
2413 2619 7.953005 TCTTGCAAATGGATTAATTGGACTA 57.047 32.000 0.00 0.00 0.00 2.59
2414 2620 7.999679 TCTTGCAAATGGATTAATTGGACTAG 58.000 34.615 0.00 0.00 0.00 2.57
2415 2621 7.833682 TCTTGCAAATGGATTAATTGGACTAGA 59.166 33.333 0.00 0.00 0.00 2.43
2416 2622 7.333528 TGCAAATGGATTAATTGGACTAGAC 57.666 36.000 0.00 0.00 0.00 2.59
2706 2915 4.568760 CGAACCTAGAAGGAGAATCAAAGC 59.431 45.833 0.00 0.00 37.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.197790 CAGAAGGGGATGCACGCG 61.198 66.667 3.53 3.53 0.00 6.01
10 11 3.512516 GCAGAAGGGGATGCACGC 61.513 66.667 0.00 0.00 42.11 5.34
11 12 2.825836 GGCAGAAGGGGATGCACG 60.826 66.667 0.00 0.00 44.37 5.34
12 13 2.440980 GGGCAGAAGGGGATGCAC 60.441 66.667 0.00 0.00 44.37 4.57
13 14 3.743017 GGGGCAGAAGGGGATGCA 61.743 66.667 0.00 0.00 44.37 3.96
14 15 4.529731 GGGGGCAGAAGGGGATGC 62.530 72.222 0.00 0.00 41.80 3.91
15 16 2.290021 GAAGGGGGCAGAAGGGGATG 62.290 65.000 0.00 0.00 0.00 3.51
16 17 2.009302 GAAGGGGGCAGAAGGGGAT 61.009 63.158 0.00 0.00 0.00 3.85
17 18 2.614013 GAAGGGGGCAGAAGGGGA 60.614 66.667 0.00 0.00 0.00 4.81
18 19 3.744155 GGAAGGGGGCAGAAGGGG 61.744 72.222 0.00 0.00 0.00 4.79
19 20 3.744155 GGGAAGGGGGCAGAAGGG 61.744 72.222 0.00 0.00 0.00 3.95
20 21 3.744155 GGGGAAGGGGGCAGAAGG 61.744 72.222 0.00 0.00 0.00 3.46
21 22 3.744155 GGGGGAAGGGGGCAGAAG 61.744 72.222 0.00 0.00 0.00 2.85
22 23 4.301662 AGGGGGAAGGGGGCAGAA 62.302 66.667 0.00 0.00 0.00 3.02
23 24 4.760220 GAGGGGGAAGGGGGCAGA 62.760 72.222 0.00 0.00 0.00 4.26
27 28 1.452226 AAAAAGGAGGGGGAAGGGGG 61.452 60.000 0.00 0.00 0.00 5.40
28 29 0.252239 CAAAAAGGAGGGGGAAGGGG 60.252 60.000 0.00 0.00 0.00 4.79
29 30 0.904865 GCAAAAAGGAGGGGGAAGGG 60.905 60.000 0.00 0.00 0.00 3.95
30 31 1.250840 CGCAAAAAGGAGGGGGAAGG 61.251 60.000 0.00 0.00 0.00 3.46
31 32 0.539669 ACGCAAAAAGGAGGGGGAAG 60.540 55.000 0.00 0.00 0.00 3.46
32 33 0.825840 CACGCAAAAAGGAGGGGGAA 60.826 55.000 0.00 0.00 0.00 3.97
33 34 1.228429 CACGCAAAAAGGAGGGGGA 60.228 57.895 0.00 0.00 0.00 4.81
34 35 1.524008 GACACGCAAAAAGGAGGGGG 61.524 60.000 0.00 0.00 0.00 5.40
35 36 1.852067 CGACACGCAAAAAGGAGGGG 61.852 60.000 0.00 0.00 0.00 4.79
36 37 1.164041 ACGACACGCAAAAAGGAGGG 61.164 55.000 0.00 0.00 0.00 4.30
37 38 0.041312 CACGACACGCAAAAAGGAGG 60.041 55.000 0.00 0.00 0.00 4.30
38 39 0.934496 TCACGACACGCAAAAAGGAG 59.066 50.000 0.00 0.00 0.00 3.69
39 40 0.653636 GTCACGACACGCAAAAAGGA 59.346 50.000 0.00 0.00 0.00 3.36
40 41 0.655733 AGTCACGACACGCAAAAAGG 59.344 50.000 0.00 0.00 0.00 3.11
41 42 1.594518 CCAGTCACGACACGCAAAAAG 60.595 52.381 0.00 0.00 0.00 2.27
42 43 0.375454 CCAGTCACGACACGCAAAAA 59.625 50.000 0.00 0.00 0.00 1.94
43 44 0.741574 ACCAGTCACGACACGCAAAA 60.742 50.000 0.00 0.00 0.00 2.44
44 45 0.102663 TACCAGTCACGACACGCAAA 59.897 50.000 0.00 0.00 0.00 3.68
45 46 0.102663 TTACCAGTCACGACACGCAA 59.897 50.000 0.00 0.00 0.00 4.85
46 47 0.102663 TTTACCAGTCACGACACGCA 59.897 50.000 0.00 0.00 0.00 5.24
47 48 1.425412 ATTTACCAGTCACGACACGC 58.575 50.000 0.00 0.00 0.00 5.34
48 49 6.301607 CGTATATATTTACCAGTCACGACACG 59.698 42.308 0.00 0.00 0.00 4.49
49 50 6.087291 GCGTATATATTTACCAGTCACGACAC 59.913 42.308 0.00 0.00 0.00 3.67
50 51 6.144854 GCGTATATATTTACCAGTCACGACA 58.855 40.000 0.00 0.00 0.00 4.35
51 52 6.144854 TGCGTATATATTTACCAGTCACGAC 58.855 40.000 0.00 0.00 0.00 4.34
52 53 6.316440 TGCGTATATATTTACCAGTCACGA 57.684 37.500 0.00 0.00 0.00 4.35
53 54 8.677871 TTATGCGTATATATTTACCAGTCACG 57.322 34.615 0.00 0.00 0.00 4.35
67 68 8.404000 CGAAGGGAGTAGTATTTATGCGTATAT 58.596 37.037 0.00 0.00 0.00 0.86
68 69 7.391554 ACGAAGGGAGTAGTATTTATGCGTATA 59.608 37.037 0.00 0.00 0.00 1.47
69 70 6.208204 ACGAAGGGAGTAGTATTTATGCGTAT 59.792 38.462 0.00 0.00 0.00 3.06
70 71 5.532406 ACGAAGGGAGTAGTATTTATGCGTA 59.468 40.000 0.00 0.00 0.00 4.42
71 72 4.340381 ACGAAGGGAGTAGTATTTATGCGT 59.660 41.667 0.00 0.00 0.00 5.24
72 73 4.868067 ACGAAGGGAGTAGTATTTATGCG 58.132 43.478 0.00 0.00 0.00 4.73
73 74 6.985059 AGAAACGAAGGGAGTAGTATTTATGC 59.015 38.462 0.00 0.00 0.00 3.14
114 115 8.794553 CCGTATGTAGTCTATAGTGGAATCTTT 58.205 37.037 0.00 0.00 0.00 2.52
115 116 8.162085 TCCGTATGTAGTCTATAGTGGAATCTT 58.838 37.037 0.00 0.00 0.00 2.40
116 117 7.687388 TCCGTATGTAGTCTATAGTGGAATCT 58.313 38.462 0.00 0.00 0.00 2.40
117 118 7.414319 GCTCCGTATGTAGTCTATAGTGGAATC 60.414 44.444 0.00 0.00 0.00 2.52
118 119 6.374894 GCTCCGTATGTAGTCTATAGTGGAAT 59.625 42.308 0.00 0.00 0.00 3.01
119 120 5.704515 GCTCCGTATGTAGTCTATAGTGGAA 59.295 44.000 0.00 0.00 0.00 3.53
120 121 5.221783 TGCTCCGTATGTAGTCTATAGTGGA 60.222 44.000 0.00 0.00 0.00 4.02
121 122 5.001874 TGCTCCGTATGTAGTCTATAGTGG 58.998 45.833 0.00 0.00 0.00 4.00
122 123 6.555812 TTGCTCCGTATGTAGTCTATAGTG 57.444 41.667 0.00 0.00 0.00 2.74
123 124 7.578310 TTTTGCTCCGTATGTAGTCTATAGT 57.422 36.000 0.00 0.00 0.00 2.12
124 125 8.297426 TCATTTTGCTCCGTATGTAGTCTATAG 58.703 37.037 0.00 0.00 0.00 1.31
125 126 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
126 127 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
127 128 6.096423 ACTCATTTTGCTCCGTATGTAGTCTA 59.904 38.462 0.00 0.00 0.00 2.59
128 129 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
129 130 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
130 131 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
131 132 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
132 133 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
133 134 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
134 135 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
135 136 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
136 137 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
137 138 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
138 139 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
139 140 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
140 141 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
151 152 7.978982 ACATGCATTTTAGAGTGTAGATTCAC 58.021 34.615 0.00 0.00 38.46 3.18
152 153 9.098355 GTACATGCATTTTAGAGTGTAGATTCA 57.902 33.333 0.00 0.00 0.00 2.57
153 154 9.098355 TGTACATGCATTTTAGAGTGTAGATTC 57.902 33.333 0.00 0.00 0.00 2.52
154 155 9.618890 ATGTACATGCATTTTAGAGTGTAGATT 57.381 29.630 7.78 0.00 0.00 2.40
156 157 9.529325 GTATGTACATGCATTTTAGAGTGTAGA 57.471 33.333 18.81 0.00 0.00 2.59
157 158 9.313118 TGTATGTACATGCATTTTAGAGTGTAG 57.687 33.333 21.01 0.00 0.00 2.74
158 159 9.830975 ATGTATGTACATGCATTTTAGAGTGTA 57.169 29.630 27.63 4.29 44.66 2.90
159 160 8.737168 ATGTATGTACATGCATTTTAGAGTGT 57.263 30.769 27.63 8.25 44.66 3.55
169 170 5.174943 CACGTACGAATGTATGTACATGCAT 59.825 40.000 27.63 27.63 46.55 3.96
170 171 4.501198 CACGTACGAATGTATGTACATGCA 59.499 41.667 25.82 25.82 46.55 3.96
171 172 4.736307 TCACGTACGAATGTATGTACATGC 59.264 41.667 24.41 17.44 46.55 4.06
172 173 6.986424 ATCACGTACGAATGTATGTACATG 57.014 37.500 24.41 4.75 46.55 3.21
173 174 7.997107 AAATCACGTACGAATGTATGTACAT 57.003 32.000 24.41 13.93 46.55 2.29
178 179 9.389570 TCACTATAAATCACGTACGAATGTATG 57.610 33.333 24.41 8.71 42.24 2.39
179 180 9.955208 TTCACTATAAATCACGTACGAATGTAT 57.045 29.630 24.41 19.31 32.11 2.29
180 181 9.786105 TTTCACTATAAATCACGTACGAATGTA 57.214 29.630 24.41 14.03 0.00 2.29
181 182 8.692110 TTTCACTATAAATCACGTACGAATGT 57.308 30.769 24.41 12.27 0.00 2.71
182 183 9.779237 GATTTCACTATAAATCACGTACGAATG 57.221 33.333 24.41 11.13 42.76 2.67
183 184 9.745880 AGATTTCACTATAAATCACGTACGAAT 57.254 29.630 24.41 12.03 44.70 3.34
184 185 9.577110 AAGATTTCACTATAAATCACGTACGAA 57.423 29.630 24.41 10.03 44.70 3.85
185 186 9.577110 AAAGATTTCACTATAAATCACGTACGA 57.423 29.630 24.41 0.00 44.70 3.43
266 267 1.073098 GGAGGGGTGGGAGAGAAAAA 58.927 55.000 0.00 0.00 0.00 1.94
267 268 0.196118 AGGAGGGGTGGGAGAGAAAA 59.804 55.000 0.00 0.00 0.00 2.29
268 269 0.196118 AAGGAGGGGTGGGAGAGAAA 59.804 55.000 0.00 0.00 0.00 2.52
269 270 0.196118 AAAGGAGGGGTGGGAGAGAA 59.804 55.000 0.00 0.00 0.00 2.87
270 271 1.098589 TAAAGGAGGGGTGGGAGAGA 58.901 55.000 0.00 0.00 0.00 3.10
271 272 1.205055 GTAAAGGAGGGGTGGGAGAG 58.795 60.000 0.00 0.00 0.00 3.20
272 273 0.797579 AGTAAAGGAGGGGTGGGAGA 59.202 55.000 0.00 0.00 0.00 3.71
273 274 1.560146 GAAGTAAAGGAGGGGTGGGAG 59.440 57.143 0.00 0.00 0.00 4.30
274 275 1.132332 TGAAGTAAAGGAGGGGTGGGA 60.132 52.381 0.00 0.00 0.00 4.37
275 276 1.368374 TGAAGTAAAGGAGGGGTGGG 58.632 55.000 0.00 0.00 0.00 4.61
276 277 2.945890 GCATGAAGTAAAGGAGGGGTGG 60.946 54.545 0.00 0.00 0.00 4.61
277 278 2.369394 GCATGAAGTAAAGGAGGGGTG 58.631 52.381 0.00 0.00 0.00 4.61
278 279 1.285078 GGCATGAAGTAAAGGAGGGGT 59.715 52.381 0.00 0.00 0.00 4.95
279 280 1.747206 CGGCATGAAGTAAAGGAGGGG 60.747 57.143 0.00 0.00 0.00 4.79
280 281 1.209504 TCGGCATGAAGTAAAGGAGGG 59.790 52.381 0.00 0.00 0.00 4.30
281 282 2.555199 CTCGGCATGAAGTAAAGGAGG 58.445 52.381 0.00 0.00 0.00 4.30
282 283 1.936547 GCTCGGCATGAAGTAAAGGAG 59.063 52.381 0.00 0.00 0.00 3.69
283 284 1.739035 CGCTCGGCATGAAGTAAAGGA 60.739 52.381 0.00 0.00 0.00 3.36
284 285 0.652592 CGCTCGGCATGAAGTAAAGG 59.347 55.000 0.00 0.00 0.00 3.11
285 286 0.026803 GCGCTCGGCATGAAGTAAAG 59.973 55.000 0.00 0.00 42.87 1.85
286 287 1.692148 CGCGCTCGGCATGAAGTAAA 61.692 55.000 5.56 0.00 43.84 2.01
287 288 2.164663 CGCGCTCGGCATGAAGTAA 61.165 57.895 5.56 0.00 43.84 2.24
308 309 3.202906 GTTTAGACAACACTGTGAGCCA 58.797 45.455 15.86 0.00 35.30 4.75
444 446 8.909671 GTGTCATTGAAGAAAGCTTGAATTTAG 58.090 33.333 0.00 0.00 36.07 1.85
445 447 7.867403 GGTGTCATTGAAGAAAGCTTGAATTTA 59.133 33.333 0.00 0.00 36.07 1.40
448 450 5.302568 TGGTGTCATTGAAGAAAGCTTGAAT 59.697 36.000 0.00 0.00 38.27 2.57
449 451 4.644234 TGGTGTCATTGAAGAAAGCTTGAA 59.356 37.500 0.00 0.00 33.61 2.69
450 452 4.036734 GTGGTGTCATTGAAGAAAGCTTGA 59.963 41.667 0.00 0.00 33.61 3.02
461 471 8.352201 CAAAATTTAGAGAAGTGGTGTCATTGA 58.648 33.333 0.00 0.00 0.00 2.57
476 486 7.718334 ATACAGGAAACCCCAAAATTTAGAG 57.282 36.000 0.00 0.00 37.41 2.43
483 493 8.499288 AAGAAAATATACAGGAAACCCCAAAA 57.501 30.769 0.00 0.00 37.41 2.44
589 611 4.142116 CCTCATGCAATTTGCTTCCATACA 60.142 41.667 21.19 0.00 45.31 2.29
616 662 8.875803 GTGAAATCACGGTACATCTATTTAACA 58.124 33.333 0.00 0.00 37.10 2.41
647 693 6.887545 TCCCATAAATCACGGTACATCTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
648 694 6.419791 TCCCATAAATCACGGTACATCTTTT 58.580 36.000 0.00 0.00 0.00 2.27
649 695 5.996644 TCCCATAAATCACGGTACATCTTT 58.003 37.500 0.00 0.00 0.00 2.52
650 696 5.130477 ACTCCCATAAATCACGGTACATCTT 59.870 40.000 0.00 0.00 0.00 2.40
683 729 8.192110 GTCTCGTTAATCTCTTCATAGTTTCCT 58.808 37.037 0.00 0.00 0.00 3.36
685 731 9.575783 AAGTCTCGTTAATCTCTTCATAGTTTC 57.424 33.333 0.00 0.00 0.00 2.78
688 734 8.514330 AGAAGTCTCGTTAATCTCTTCATAGT 57.486 34.615 0.00 0.00 35.30 2.12
689 735 9.796120 AAAGAAGTCTCGTTAATCTCTTCATAG 57.204 33.333 0.00 0.00 35.30 2.23
690 736 9.790389 GAAAGAAGTCTCGTTAATCTCTTCATA 57.210 33.333 0.00 0.00 35.30 2.15
691 737 8.527810 AGAAAGAAGTCTCGTTAATCTCTTCAT 58.472 33.333 0.00 0.00 35.30 2.57
693 739 8.389586 GAGAAAGAAGTCTCGTTAATCTCTTC 57.610 38.462 0.00 0.00 35.04 2.87
705 751 9.497030 GAAAAACTCAAAAGAGAAAGAAGTCTC 57.503 33.333 0.00 0.00 43.80 3.36
707 753 9.283420 CAGAAAAACTCAAAAGAGAAAGAAGTC 57.717 33.333 0.00 0.00 0.00 3.01
709 755 7.221645 GCCAGAAAAACTCAAAAGAGAAAGAAG 59.778 37.037 0.00 0.00 0.00 2.85
710 756 7.035612 GCCAGAAAAACTCAAAAGAGAAAGAA 58.964 34.615 0.00 0.00 0.00 2.52
711 757 6.564328 GCCAGAAAAACTCAAAAGAGAAAGA 58.436 36.000 0.00 0.00 0.00 2.52
712 758 5.456822 CGCCAGAAAAACTCAAAAGAGAAAG 59.543 40.000 0.00 0.00 0.00 2.62
714 760 4.202010 CCGCCAGAAAAACTCAAAAGAGAA 60.202 41.667 0.00 0.00 0.00 2.87
718 764 3.372060 GTCCGCCAGAAAAACTCAAAAG 58.628 45.455 0.00 0.00 0.00 2.27
720 766 1.679153 GGTCCGCCAGAAAAACTCAAA 59.321 47.619 0.00 0.00 34.09 2.69
722 768 0.472471 AGGTCCGCCAGAAAAACTCA 59.528 50.000 0.00 0.00 37.19 3.41
726 772 0.882927 CGACAGGTCCGCCAGAAAAA 60.883 55.000 0.00 0.00 37.19 1.94
735 781 3.989698 ATCTTGCGCGACAGGTCCG 62.990 63.158 12.10 6.11 0.00 4.79
737 783 0.737715 AAGATCTTGCGCGACAGGTC 60.738 55.000 12.10 10.51 0.00 3.85
738 784 0.320771 AAAGATCTTGCGCGACAGGT 60.321 50.000 12.10 0.00 0.00 4.00
739 785 0.095935 CAAAGATCTTGCGCGACAGG 59.904 55.000 12.10 8.42 0.00 4.00
742 788 0.095417 GACCAAAGATCTTGCGCGAC 59.905 55.000 12.10 0.88 0.00 5.19
743 789 0.037326 AGACCAAAGATCTTGCGCGA 60.037 50.000 12.10 0.00 0.00 5.87
744 790 0.798776 AAGACCAAAGATCTTGCGCG 59.201 50.000 9.17 0.00 35.06 6.86
745 791 1.131315 GGAAGACCAAAGATCTTGCGC 59.869 52.381 9.17 0.00 36.53 6.09
746 792 1.740025 GGGAAGACCAAAGATCTTGCG 59.260 52.381 9.17 4.62 43.37 4.85
747 793 2.095461 GGGGAAGACCAAAGATCTTGC 58.905 52.381 9.17 0.00 42.14 4.01
748 794 3.009473 TCAGGGGAAGACCAAAGATCTTG 59.991 47.826 9.17 0.00 42.91 3.02
752 798 3.500471 GGTTTCAGGGGAAGACCAAAGAT 60.500 47.826 0.00 0.00 42.91 2.40
753 799 2.158519 GGTTTCAGGGGAAGACCAAAGA 60.159 50.000 0.00 0.00 42.91 2.52
754 800 2.239400 GGTTTCAGGGGAAGACCAAAG 58.761 52.381 0.00 0.00 42.91 2.77
755 801 1.477923 CGGTTTCAGGGGAAGACCAAA 60.478 52.381 0.00 0.00 42.91 3.28
756 802 0.109723 CGGTTTCAGGGGAAGACCAA 59.890 55.000 0.00 0.00 42.91 3.67
759 805 1.278127 TCATCGGTTTCAGGGGAAGAC 59.722 52.381 0.00 0.00 33.82 3.01
760 806 1.651737 TCATCGGTTTCAGGGGAAGA 58.348 50.000 0.00 0.00 33.82 2.87
761 807 2.489938 TTCATCGGTTTCAGGGGAAG 57.510 50.000 0.00 0.00 33.82 3.46
762 808 2.961531 TTTCATCGGTTTCAGGGGAA 57.038 45.000 0.00 0.00 0.00 3.97
763 809 2.961531 TTTTCATCGGTTTCAGGGGA 57.038 45.000 0.00 0.00 0.00 4.81
827 916 3.021177 ACCCAATGCATGATCACATCA 57.979 42.857 0.00 0.00 44.55 3.07
843 932 1.847890 GCAAGCGCTACGAAAACCCA 61.848 55.000 12.05 0.00 34.30 4.51
920 1016 1.740296 CGGTGGTCGTGATGGGAAC 60.740 63.158 0.00 0.00 0.00 3.62
943 1039 2.225963 CCAAGAGGTAGGATACGCGTAG 59.774 54.545 24.78 5.97 44.28 3.51
950 1046 1.497716 TCGAGCCCAAGAGGTAGGATA 59.502 52.381 0.00 0.00 38.26 2.59
1156 1253 1.545428 GGAGAAATGGCGGCCATGATA 60.545 52.381 33.56 6.89 44.40 2.15
1212 1309 7.663664 CACTCACGACAAATATGTACAAGTAC 58.336 38.462 0.00 3.47 40.74 2.73
1491 1603 3.913573 GTCATAGGCACGCACGCG 61.914 66.667 10.36 10.36 46.03 6.01
1524 1640 2.041701 AGCACCTGCAACCAAGAAAAT 58.958 42.857 0.00 0.00 45.16 1.82
1622 1739 7.686438 TCAACACACAGCATAAGTTGATTAT 57.314 32.000 0.00 0.00 42.35 1.28
1635 1752 0.953727 TCAAGGCATCAACACACAGC 59.046 50.000 0.00 0.00 0.00 4.40
1636 1753 3.079578 AGATCAAGGCATCAACACACAG 58.920 45.455 0.00 0.00 0.00 3.66
1735 1871 1.730064 GACGCCAACGAAAGAATAGCA 59.270 47.619 0.00 0.00 43.93 3.49
1821 1958 5.391577 ACTTAAAACCCTGACACCCTAAA 57.608 39.130 0.00 0.00 0.00 1.85
1831 1985 4.091509 CGATCGACTCAACTTAAAACCCTG 59.908 45.833 10.26 0.00 0.00 4.45
1860 2014 5.940192 ATTGCGTTGAACTTGACTATGAA 57.060 34.783 0.00 0.00 0.00 2.57
1876 2030 4.272504 CCGGACTGACATTTTATATTGCGT 59.727 41.667 0.00 0.00 0.00 5.24
1905 2061 4.499037 AAAACAGGTTGCGAAGGATTAC 57.501 40.909 0.00 0.00 0.00 1.89
1928 2084 8.581253 AAACTGAGAAGAAAAAGAAGAAGGAA 57.419 30.769 0.00 0.00 0.00 3.36
1929 2085 8.581253 AAAACTGAGAAGAAAAAGAAGAAGGA 57.419 30.769 0.00 0.00 0.00 3.36
2148 2312 8.821147 ACAATATAAAATTGCATGCCATACAG 57.179 30.769 16.68 2.90 32.55 2.74
2193 2357 0.108585 TCCAACTGTTCCTGGTCAGC 59.891 55.000 16.74 0.00 35.37 4.26
2201 2365 1.605753 GGGTTCTGTCCAACTGTTCC 58.394 55.000 0.00 0.00 0.00 3.62
2266 2439 8.893563 TGTTTCCCCATTTAGAATTTGTATCT 57.106 30.769 0.00 0.00 0.00 1.98
2280 2453 6.256053 AGACATACTTTGATGTTTCCCCATT 58.744 36.000 0.00 0.00 40.18 3.16
2293 2499 7.759886 TGGATTTTCTCGACTAGACATACTTTG 59.240 37.037 0.00 0.00 32.51 2.77
2390 2596 7.917505 GTCTAGTCCAATTAATCCATTTGCAAG 59.082 37.037 0.00 0.00 0.00 4.01
2391 2597 7.415095 CGTCTAGTCCAATTAATCCATTTGCAA 60.415 37.037 0.00 0.00 0.00 4.08
2393 2599 6.260050 TCGTCTAGTCCAATTAATCCATTTGC 59.740 38.462 0.00 0.00 0.00 3.68
2394 2600 7.495934 AGTCGTCTAGTCCAATTAATCCATTTG 59.504 37.037 0.00 0.00 0.00 2.32
2395 2601 7.565680 AGTCGTCTAGTCCAATTAATCCATTT 58.434 34.615 0.00 0.00 0.00 2.32
2411 2617 4.643784 ACAATGGGGTAACTAGTCGTCTAG 59.356 45.833 14.10 14.10 46.43 2.43
2412 2618 4.400251 CACAATGGGGTAACTAGTCGTCTA 59.600 45.833 0.00 0.00 0.00 2.59
2413 2619 3.194968 CACAATGGGGTAACTAGTCGTCT 59.805 47.826 0.00 0.00 0.00 4.18
2414 2620 3.056322 ACACAATGGGGTAACTAGTCGTC 60.056 47.826 0.00 0.00 0.00 4.20
2415 2621 2.901839 ACACAATGGGGTAACTAGTCGT 59.098 45.455 0.00 0.00 0.00 4.34
2416 2622 3.604875 ACACAATGGGGTAACTAGTCG 57.395 47.619 0.00 0.00 0.00 4.18
2431 2637 8.103973 CAGGTTACTGCACATTGTTTTACACAA 61.104 37.037 0.00 0.00 42.92 3.33
2465 2671 0.657840 GCAATGCACTGGGTATCGTC 59.342 55.000 0.00 0.00 0.00 4.20
2602 2808 9.557061 CCCTAAGTGGAATTATTTACTTACTCC 57.443 37.037 9.89 0.00 38.35 3.85
2604 2810 8.500238 CCCCCTAAGTGGAATTATTTACTTACT 58.500 37.037 9.89 0.00 38.35 2.24
2605 2811 8.277197 ACCCCCTAAGTGGAATTATTTACTTAC 58.723 37.037 9.89 0.00 38.35 2.34
2606 2812 8.410000 ACCCCCTAAGTGGAATTATTTACTTA 57.590 34.615 12.05 12.05 38.35 2.24
2619 2827 2.104963 GCTAATGAGACCCCCTAAGTGG 59.895 54.545 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.