Multiple sequence alignment - TraesCS5D01G071000

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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 TraesCS5D01G071000 chr5D 100.000 7802 0 0 1 7802 69102706 69094905 0.000000e+00 14408.0
1 TraesCS5D01G071000 chr5D 85.227 176 21 2 6138 6312 230372137 230371966 8.050000e-40 176.0
2 TraesCS5D01G071000 chr5D 84.211 171 22 3 6142 6312 492238158 492238323 2.250000e-35 161.0
3 TraesCS5D01G071000 chr5D 100.000 57 0 0 7657 7713 166726252 166726308 1.070000e-18 106.0
4 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 6253629 6253686 2.320000e-15 95.3
5 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 299972862 299972919 2.320000e-15 95.3
6 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 503313153 503313096 2.320000e-15 95.3
7 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 503339086 503339029 2.320000e-15 95.3
8 TraesCS5D01G071000 chr5D 97.059 34 1 0 6418 6451 483574146 483574179 3.040000e-04 58.4
9 TraesCS5D01G071000 chr5A 95.352 4690 154 26 1 4647 59707220 59702552 0.000000e+00 7395.0
10 TraesCS5D01G071000 chr5A 96.605 1237 29 9 4897 6128 59702229 59701001 0.000000e+00 2039.0
11 TraesCS5D01G071000 chr5A 89.703 1214 65 34 6456 7654 59700717 59699549 0.000000e+00 1495.0
12 TraesCS5D01G071000 chr5A 94.915 236 11 1 4657 4891 59702507 59702272 1.240000e-97 368.0
13 TraesCS5D01G071000 chr5A 94.681 188 9 1 6200 6386 59701004 59700817 2.750000e-74 291.0
14 TraesCS5D01G071000 chr5A 92.373 118 7 2 6024 6141 59700889 59701004 4.840000e-37 167.0
15 TraesCS5D01G071000 chr5A 77.990 209 34 8 7290 7487 504873961 504873754 3.820000e-23 121.0
16 TraesCS5D01G071000 chr5B 94.477 3404 105 26 1 3353 74995357 74991986 0.000000e+00 5168.0
17 TraesCS5D01G071000 chr5B 96.879 3012 56 10 3351 6356 74991825 74988846 0.000000e+00 5007.0
18 TraesCS5D01G071000 chr5B 90.271 1182 69 18 6417 7554 74988884 74987705 0.000000e+00 1504.0
19 TraesCS5D01G071000 chr5B 97.297 37 1 0 6419 6455 479643539 479643575 6.540000e-06 63.9
20 TraesCS5D01G071000 chr4B 86.420 486 50 11 3953 4431 462214596 462215072 1.160000e-142 518.0
21 TraesCS5D01G071000 chr4B 80.216 556 73 18 2694 3241 462213472 462213998 4.420000e-102 383.0
22 TraesCS5D01G071000 chr4B 81.327 407 52 15 3507 3909 462214211 462214597 7.600000e-80 309.0
23 TraesCS5D01G071000 chr4B 84.302 172 26 1 1334 1504 63757634 63757463 4.840000e-37 167.0
24 TraesCS5D01G071000 chr4B 91.304 115 8 2 6027 6141 525389930 525390042 1.050000e-33 156.0
25 TraesCS5D01G071000 chr4B 96.552 58 1 1 7746 7802 77367842 77367785 2.320000e-15 95.3
26 TraesCS5D01G071000 chr4D 82.321 560 74 15 2694 3244 375120895 375121438 5.520000e-126 462.0
27 TraesCS5D01G071000 chr4D 82.384 562 61 26 3953 4484 375121945 375122498 9.230000e-124 455.0
28 TraesCS5D01G071000 chr4D 81.714 525 60 20 3389 3909 375121454 375121946 9.430000e-109 405.0
29 TraesCS5D01G071000 chr4D 91.391 151 11 2 4761 4910 220008794 220008645 1.030000e-48 206.0
30 TraesCS5D01G071000 chr4D 82.955 176 29 1 1334 1508 43652140 43651965 2.910000e-34 158.0
31 TraesCS5D01G071000 chr4D 79.487 195 29 9 6199 6386 490889533 490889723 2.290000e-25 128.0
32 TraesCS5D01G071000 chr4D 95.455 66 3 0 6321 6386 50156124 50156059 1.070000e-18 106.0
33 TraesCS5D01G071000 chr4D 100.000 33 0 0 7714 7746 18320726 18320758 2.350000e-05 62.1
34 TraesCS5D01G071000 chr4D 100.000 33 0 0 7714 7746 35179180 35179212 2.350000e-05 62.1
35 TraesCS5D01G071000 chr4D 94.872 39 2 0 6417 6455 320026965 320027003 2.350000e-05 62.1
36 TraesCS5D01G071000 chr4D 96.970 33 1 0 6420 6452 507484159 507484191 1.000000e-03 56.5
37 TraesCS5D01G071000 chr4A 81.879 298 35 11 2950 3244 89447028 89446747 4.710000e-57 233.0
38 TraesCS5D01G071000 chr4A 96.183 131 5 0 4761 4891 115567072 115567202 1.710000e-51 215.0
39 TraesCS5D01G071000 chr4A 92.667 150 10 1 4761 4910 664908870 664909018 1.710000e-51 215.0
40 TraesCS5D01G071000 chr4A 87.135 171 18 2 6142 6312 89430875 89431041 2.870000e-44 191.0
41 TraesCS5D01G071000 chr4A 84.211 171 23 2 6142 6312 8966095 8965929 6.260000e-36 163.0
42 TraesCS5D01G071000 chr4A 82.558 172 29 1 1334 1504 556251108 556251279 4.880000e-32 150.0
43 TraesCS5D01G071000 chr4A 81.529 157 21 7 2750 2902 89447175 89447023 1.060000e-23 122.0
44 TraesCS5D01G071000 chr4A 92.308 78 5 1 6310 6386 618462270 618462193 8.280000e-20 110.0
45 TraesCS5D01G071000 chr7B 95.489 133 5 1 4761 4892 639069546 639069678 2.210000e-50 211.0
46 TraesCS5D01G071000 chr7B 92.308 143 10 1 4765 4907 461227482 461227341 1.330000e-47 202.0
47 TraesCS5D01G071000 chr7B 97.297 37 1 0 6419 6455 625725344 625725308 6.540000e-06 63.9
48 TraesCS5D01G071000 chr6B 92.105 152 9 3 4761 4910 225550093 225550243 2.210000e-50 211.0
49 TraesCS5D01G071000 chr6B 97.015 67 2 0 6320 6386 675195026 675195092 6.400000e-21 113.0
50 TraesCS5D01G071000 chr2B 91.391 151 12 1 4761 4910 183534793 183534643 1.030000e-48 206.0
51 TraesCS5D01G071000 chr2B 84.946 93 10 3 6290 6381 799358710 799358799 3.000000e-14 91.6
52 TraesCS5D01G071000 chr2B 100.000 30 0 0 7296 7325 111677184 111677213 1.000000e-03 56.5
53 TraesCS5D01G071000 chr7A 88.304 171 16 3 6142 6312 26885310 26885476 1.330000e-47 202.0
54 TraesCS5D01G071000 chr2D 87.135 171 18 1 6142 6312 325325475 325325641 2.870000e-44 191.0
55 TraesCS5D01G071000 chr7D 85.542 166 19 4 6147 6312 133308264 133308424 1.350000e-37 169.0
56 TraesCS5D01G071000 chr7D 88.333 120 11 3 6023 6141 613824181 613824064 2.940000e-29 141.0
57 TraesCS5D01G071000 chr7D 100.000 57 0 0 7657 7713 6949297 6949353 1.070000e-18 106.0
58 TraesCS5D01G071000 chr7D 100.000 57 0 0 7657 7713 607304143 607304087 1.070000e-18 106.0
59 TraesCS5D01G071000 chr1B 84.483 174 23 1 6142 6315 37625407 37625576 1.350000e-37 169.0
60 TraesCS5D01G071000 chr1B 97.297 37 1 0 6419 6455 222194510 222194546 6.540000e-06 63.9
61 TraesCS5D01G071000 chr1B 95.122 41 1 1 6416 6455 477403822 477403862 6.540000e-06 63.9
62 TraesCS5D01G071000 chr1B 97.222 36 1 0 6420 6455 322473484 322473519 2.350000e-05 62.1
63 TraesCS5D01G071000 chr3B 90.435 115 9 2 6027 6141 482258709 482258821 4.880000e-32 150.0
64 TraesCS5D01G071000 chr3B 86.525 141 14 5 6001 6141 704132053 704132188 4.880000e-32 150.0
65 TraesCS5D01G071000 chr3B 89.815 108 11 0 6034 6141 704132310 704132203 1.060000e-28 139.0
66 TraesCS5D01G071000 chrUn 85.385 130 13 6 6021 6147 186637995 186637869 6.350000e-26 130.0
67 TraesCS5D01G071000 chrUn 96.552 58 1 1 7746 7802 445187753 445187696 2.320000e-15 95.3
68 TraesCS5D01G071000 chrUn 96.552 58 1 1 7746 7802 455659533 455659476 2.320000e-15 95.3
69 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 216510016 216509984 2.350000e-05 62.1
70 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 390488898 390488930 2.350000e-05 62.1
71 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 397078202 397078170 2.350000e-05 62.1
72 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 424751053 424751021 2.350000e-05 62.1
73 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 455551994 455552026 2.350000e-05 62.1
74 TraesCS5D01G071000 chr3A 93.333 75 4 1 6313 6386 507291481 507291555 8.280000e-20 110.0
75 TraesCS5D01G071000 chr3A 100.000 57 0 0 7657 7713 227626105 227626049 1.070000e-18 106.0
76 TraesCS5D01G071000 chr3A 87.273 55 6 1 6420 6473 543729615 543729669 2.350000e-05 62.1
77 TraesCS5D01G071000 chr1D 100.000 57 0 0 7657 7713 493808975 493808919 1.070000e-18 106.0
78 TraesCS5D01G071000 chr1D 98.246 57 1 0 7746 7802 51832314 51832370 4.980000e-17 100.0
79 TraesCS5D01G071000 chr1D 97.222 36 1 0 6420 6455 223162273 223162308 2.350000e-05 62.1
80 TraesCS5D01G071000 chr1D 100.000 28 0 0 6423 6450 243461247 243461220 1.400000e-02 52.8
81 TraesCS5D01G071000 chr1A 94.286 70 3 1 6321 6390 135508399 135508467 1.070000e-18 106.0
82 TraesCS5D01G071000 chr1A 98.246 57 1 0 7657 7713 94702512 94702456 4.980000e-17 100.0
83 TraesCS5D01G071000 chr1A 98.246 57 0 1 7657 7713 94531383 94531438 1.790000e-16 99.0
84 TraesCS5D01G071000 chr1A 96.552 58 1 1 7746 7802 554481903 554481846 2.320000e-15 95.3
85 TraesCS5D01G071000 chr1A 95.122 41 1 1 6416 6455 382550778 382550738 6.540000e-06 63.9
86 TraesCS5D01G071000 chr1A 97.222 36 1 0 6420 6455 290124419 290124454 2.350000e-05 62.1
87 TraesCS5D01G071000 chr1A 94.872 39 2 0 6417 6455 436259650 436259688 2.350000e-05 62.1
88 TraesCS5D01G071000 chr3D 98.246 57 1 0 7657 7713 213392396 213392452 4.980000e-17 100.0
89 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 457058472 457058508 6.540000e-06 63.9
90 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 570105968 570105932 6.540000e-06 63.9
91 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 582778867 582778831 6.540000e-06 63.9
92 TraesCS5D01G071000 chr6A 98.246 57 0 1 7657 7713 375844681 375844736 1.790000e-16 99.0
93 TraesCS5D01G071000 chr6A 97.222 36 1 0 6420 6455 356112246 356112281 2.350000e-05 62.1
94 TraesCS5D01G071000 chr6A 100.000 32 0 0 6424 6455 393802364 393802333 8.450000e-05 60.2
95 TraesCS5D01G071000 chr6D 100.000 33 0 0 7714 7746 389248477 389248509 2.350000e-05 62.1
96 TraesCS5D01G071000 chr6D 100.000 33 0 0 7714 7746 389253272 389253304 2.350000e-05 62.1


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 TraesCS5D01G071000 chr5D 69094905 69102706 7801 True 14408.000000 14408 100.000000 1 7802 1 chr5D.!!$R1 7801
1 TraesCS5D01G071000 chr5A 59699549 59707220 7671 True 2317.600000 7395 94.251200 1 7654 5 chr5A.!!$R2 7653
2 TraesCS5D01G071000 chr5B 74987705 74995357 7652 True 3893.000000 5168 93.875667 1 7554 3 chr5B.!!$R1 7553
3 TraesCS5D01G071000 chr4B 462213472 462215072 1600 False 403.333333 518 82.654333 2694 4431 3 chr4B.!!$F2 1737
4 TraesCS5D01G071000 chr4D 375120895 375122498 1603 False 440.666667 462 82.139667 2694 4484 3 chr4D.!!$F6 1790

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
582 609 0.378257 CGCTCTGCACTCTCTCTCTC 59.622 60.000 0.00 0.00 0.00 3.20 F
583 610 1.755179 GCTCTGCACTCTCTCTCTCT 58.245 55.000 0.00 0.00 0.00 3.10 F
1185 1260 2.158827 GGAACCCAAAGGCACAAACAAT 60.159 45.455 0.00 0.00 36.11 2.71 F
1811 1890 3.079578 CTGTGTTGATGTGCCTTCTCAT 58.920 45.455 0.00 0.00 0.00 2.90 F
1928 2007 4.657952 GGCAACGGAAGGCCTTAT 57.342 55.556 20.54 3.99 46.74 1.73 F
3490 3754 2.132740 TTGGCAGTTTCATTTCACGC 57.867 45.000 0.00 0.00 0.00 5.34 F
4011 4362 0.917533 AGGATGAGCCAGATGCACTT 59.082 50.000 0.00 0.00 44.83 3.16 F
4551 4936 1.577468 TTTCGTGACTGATTGTGCGT 58.423 45.000 0.00 0.00 0.00 5.24 F
5112 5573 1.143684 ACAGAGAATGTGCCACCTGTT 59.856 47.619 0.00 0.00 41.91 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2422 1.458639 GCTTGCTCCTTGCTGGTTGT 61.459 55.000 0.00 0.0 43.37 3.32 R
2569 2652 4.672587 ATAAATCTGGAAGCTCGCTACA 57.327 40.909 0.00 0.0 0.00 2.74 R
3180 3281 1.237285 ACTTGCTGTTGACGGGCATC 61.237 55.000 0.00 0.0 35.84 3.91 R
3319 3420 3.840078 CCCAGAAATTTCCCATCCAACTT 59.160 43.478 14.61 0.0 0.00 2.66 R
3625 3974 7.667219 TGGGCAGATTTTAGAATATCAATCCTC 59.333 37.037 0.00 0.0 0.00 3.71 R
4682 5103 1.708341 AGGGCAAGCTTTTGTCATGT 58.292 45.000 0.00 0.0 0.00 3.21 R
4885 5309 2.741145 ACAACAACAAAGCCTGGGTAA 58.259 42.857 0.00 0.0 0.00 2.85 R
6414 6878 0.396811 GGGACGGAGGGATTACATGG 59.603 60.000 0.00 0.0 0.00 3.66 R
6837 7334 0.249280 CAGGCCGAACAACAAAACCC 60.249 55.000 0.00 0.0 0.00 4.11 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
248 256 1.731160 ACCACGAAACAAACGAACGAA 59.269 42.857 0.14 0.00 34.70 3.85
383 401 1.065701 CCGCCGCAGCTAGTATATAGG 59.934 57.143 0.00 0.00 36.60 2.57
579 606 0.607762 TCACGCTCTGCACTCTCTCT 60.608 55.000 0.00 0.00 0.00 3.10
582 609 0.378257 CGCTCTGCACTCTCTCTCTC 59.622 60.000 0.00 0.00 0.00 3.20
583 610 1.755179 GCTCTGCACTCTCTCTCTCT 58.245 55.000 0.00 0.00 0.00 3.10
601 628 2.826287 CTCTCCCTCTCGCTCGCA 60.826 66.667 0.00 0.00 0.00 5.10
808 882 3.650369 CGCTTAGGGTTTGCGTGT 58.350 55.556 0.00 0.00 44.00 4.49
822 896 3.845259 GTGTGGATCCGCGGCCTA 61.845 66.667 23.51 10.03 0.00 3.93
838 912 2.555199 GCCTATGTGCTTAGTGAGGTG 58.445 52.381 0.00 0.00 0.00 4.00
957 1032 5.551233 TGTGCAGAGAGTTTATGCTACTTT 58.449 37.500 1.72 0.00 40.62 2.66
1185 1260 2.158827 GGAACCCAAAGGCACAAACAAT 60.159 45.455 0.00 0.00 36.11 2.71
1522 1600 6.410540 AGTTCTTCATTCTCTTGTACCATCC 58.589 40.000 0.00 0.00 0.00 3.51
1540 1618 5.997746 ACCATCCTGGATTGTTATTATCACG 59.002 40.000 6.42 0.00 40.96 4.35
1612 1690 3.803778 GTGAAAGCCAAGGTTGATTTGTG 59.196 43.478 0.00 0.00 0.00 3.33
1625 1703 4.787135 TGATTTGTGGCCCATATCAGTA 57.213 40.909 17.27 2.93 36.83 2.74
1628 1706 6.135454 TGATTTGTGGCCCATATCAGTATTT 58.865 36.000 17.27 0.00 36.83 1.40
1680 1759 5.036117 ACGATGCAGAGGTATATTGGTTT 57.964 39.130 0.00 0.00 0.00 3.27
1772 1851 9.682465 CTATATGGTAGCTATAGGACTGTACAA 57.318 37.037 0.00 0.00 0.00 2.41
1811 1890 3.079578 CTGTGTTGATGTGCCTTCTCAT 58.920 45.455 0.00 0.00 0.00 2.90
1822 1901 8.843262 TGATGTGCCTTCTCATATTCTTATTTG 58.157 33.333 0.00 0.00 0.00 2.32
1845 1924 4.770795 CCGGGTTATCAGAAGTTCAGAAT 58.229 43.478 5.50 0.00 0.00 2.40
1856 1935 7.864686 TCAGAAGTTCAGAATGTTTGTGTATG 58.135 34.615 5.50 0.00 37.40 2.39
1878 1957 6.036577 TGTGTTGTCTTGATGTGCTATAGA 57.963 37.500 3.21 0.00 0.00 1.98
1879 1958 5.869344 TGTGTTGTCTTGATGTGCTATAGAC 59.131 40.000 3.21 0.00 36.61 2.59
1880 1959 6.102663 GTGTTGTCTTGATGTGCTATAGACT 58.897 40.000 3.21 0.00 36.91 3.24
1881 1960 7.093945 TGTGTTGTCTTGATGTGCTATAGACTA 60.094 37.037 3.21 0.00 36.91 2.59
1882 1961 7.923344 GTGTTGTCTTGATGTGCTATAGACTAT 59.077 37.037 3.21 0.00 36.91 2.12
1883 1962 9.131791 TGTTGTCTTGATGTGCTATAGACTATA 57.868 33.333 3.21 2.24 36.91 1.31
1884 1963 9.619316 GTTGTCTTGATGTGCTATAGACTATAG 57.381 37.037 20.87 20.87 40.83 1.31
1928 2007 4.657952 GGCAACGGAAGGCCTTAT 57.342 55.556 20.54 3.99 46.74 1.73
2214 2295 7.335422 CACTGCTAAATCAGACTGAAGGTTTAT 59.665 37.037 9.70 0.00 37.51 1.40
2308 2390 5.187576 ACAATGCAATATTAACCACCTGCTT 59.812 36.000 0.00 0.00 0.00 3.91
2309 2391 6.379703 ACAATGCAATATTAACCACCTGCTTA 59.620 34.615 0.00 0.00 0.00 3.09
2552 2635 6.292919 GCTATCGGCCAACTTAAGAACATTAG 60.293 42.308 10.09 1.70 34.27 1.73
2769 2864 5.685841 CACAAGTATGGAACCTGTAAAACG 58.314 41.667 0.00 0.00 30.74 3.60
3151 3252 7.391554 CCTAGATGGTTCTTTCAGAAAATGACA 59.608 37.037 0.00 0.00 35.75 3.58
3217 3318 9.717942 ACAGCAAGTAAAAATGCCATTTATAAA 57.282 25.926 2.54 0.00 43.57 1.40
3456 3720 2.235016 TGGGAACACATAGTTTGGCAC 58.765 47.619 0.00 0.00 41.51 5.01
3481 3745 8.515414 ACTCTGATTACTTTAATTGGCAGTTTC 58.485 33.333 0.00 0.00 0.00 2.78
3489 3753 6.420604 ACTTTAATTGGCAGTTTCATTTCACG 59.579 34.615 0.00 0.00 0.00 4.35
3490 3754 2.132740 TTGGCAGTTTCATTTCACGC 57.867 45.000 0.00 0.00 0.00 5.34
3625 3974 7.595819 TGGATAAATTGTGCTAAAATAGGGG 57.404 36.000 0.00 0.00 0.00 4.79
3815 4165 6.150976 TGTGGTCATTTCATCATCCAACTAAC 59.849 38.462 0.00 0.00 0.00 2.34
3871 4222 3.249320 CCATATTGTGTCTCCTCAATGCG 59.751 47.826 0.00 0.00 35.97 4.73
3990 4341 6.747280 CCTGTTTAAAGGTAATGATTTCAGCG 59.253 38.462 0.00 0.00 32.17 5.18
4011 4362 0.917533 AGGATGAGCCAGATGCACTT 59.082 50.000 0.00 0.00 44.83 3.16
4044 4395 2.756840 TTGATGGTCTGCTCAGAGTG 57.243 50.000 0.00 0.00 38.27 3.51
4200 4551 7.080099 CCATTAAATCAATACAGGATGCTTCG 58.920 38.462 0.00 0.00 42.53 3.79
4327 4688 8.417884 ACCTATTCTGCTCTTGATACTAAGTTC 58.582 37.037 0.00 0.00 0.00 3.01
4537 4922 7.696992 TCCAAATTATTTCCTAGCTTTTCGT 57.303 32.000 0.00 0.00 0.00 3.85
4551 4936 1.577468 TTTCGTGACTGATTGTGCGT 58.423 45.000 0.00 0.00 0.00 5.24
4568 4953 2.557490 TGCGTGTACAGTGTACCATACA 59.443 45.455 26.66 17.59 36.08 2.29
4682 5103 9.716531 TTTTAAAATATGGAATTCATGCACACA 57.283 25.926 7.93 0.00 37.30 3.72
4711 5132 7.061566 ACAAAAGCTTGCCCTTTAAGAATTA 57.938 32.000 0.00 0.00 35.84 1.40
4857 5281 2.040145 TGCCAGAATCATGAGTTGGTCA 59.960 45.455 18.82 15.43 40.38 4.02
4885 5309 4.362677 TCTTATGGGTTTCACCTCTAGCT 58.637 43.478 0.00 0.00 38.64 3.32
4924 5385 7.056002 TGTTGTTGTTATGCTAGAATGTACG 57.944 36.000 0.00 0.00 0.00 3.67
5112 5573 1.143684 ACAGAGAATGTGCCACCTGTT 59.856 47.619 0.00 0.00 41.91 3.16
5268 5729 7.227314 CAGGTAAGTGATTTCTATTATGCAGCA 59.773 37.037 0.00 0.00 0.00 4.41
5586 6047 3.852578 ACCTCAGGGAATCAACACCTATT 59.147 43.478 0.00 0.00 36.25 1.73
6097 6560 8.259049 TCTAAGTTTGACCATACATTTAACCG 57.741 34.615 0.00 0.00 0.00 4.44
6111 6574 1.915614 TAACCGACGAGACCGACTGC 61.916 60.000 0.00 0.00 39.50 4.40
6125 6588 1.795170 GACTGCGGCAGGAGCAAAAA 61.795 55.000 31.38 0.00 44.67 1.94
6175 6638 4.920376 CGGGAGCAAAAATTATACCACTG 58.080 43.478 0.00 0.00 0.00 3.66
6176 6639 4.638421 CGGGAGCAAAAATTATACCACTGA 59.362 41.667 0.00 0.00 0.00 3.41
6177 6640 5.124776 CGGGAGCAAAAATTATACCACTGAA 59.875 40.000 0.00 0.00 0.00 3.02
6178 6641 6.183360 CGGGAGCAAAAATTATACCACTGAAT 60.183 38.462 0.00 0.00 0.00 2.57
6179 6642 7.555965 GGGAGCAAAAATTATACCACTGAATT 58.444 34.615 0.00 0.00 0.00 2.17
6180 6643 7.706607 GGGAGCAAAAATTATACCACTGAATTC 59.293 37.037 0.00 0.00 0.00 2.17
6181 6644 8.250332 GGAGCAAAAATTATACCACTGAATTCA 58.750 33.333 8.12 8.12 0.00 2.57
6381 6845 2.916111 ACATAGCTTGCAAAAACGTCG 58.084 42.857 0.00 0.00 0.00 5.12
6386 6850 4.735662 AGCTTGCAAAAACGTCGTATAA 57.264 36.364 0.00 0.00 0.00 0.98
6387 6851 5.098218 AGCTTGCAAAAACGTCGTATAAA 57.902 34.783 0.00 0.00 0.00 1.40
6388 6852 5.512473 AGCTTGCAAAAACGTCGTATAAAA 58.488 33.333 0.00 0.00 0.00 1.52
6389 6853 5.397240 AGCTTGCAAAAACGTCGTATAAAAC 59.603 36.000 0.00 0.00 0.00 2.43
6390 6854 5.386627 GCTTGCAAAAACGTCGTATAAAACC 60.387 40.000 0.00 0.00 0.00 3.27
6391 6855 4.535116 TGCAAAAACGTCGTATAAAACCC 58.465 39.130 0.00 0.00 0.00 4.11
6392 6856 3.913763 GCAAAAACGTCGTATAAAACCCC 59.086 43.478 0.00 0.00 0.00 4.95
6393 6857 4.475028 CAAAAACGTCGTATAAAACCCCC 58.525 43.478 0.00 0.00 0.00 5.40
6394 6858 3.701205 AAACGTCGTATAAAACCCCCT 57.299 42.857 0.00 0.00 0.00 4.79
6395 6859 3.701205 AACGTCGTATAAAACCCCCTT 57.299 42.857 0.00 0.00 0.00 3.95
6396 6860 3.701205 ACGTCGTATAAAACCCCCTTT 57.299 42.857 0.00 0.00 0.00 3.11
6398 6862 5.159273 ACGTCGTATAAAACCCCCTTTAA 57.841 39.130 0.00 0.00 0.00 1.52
6400 6864 5.178061 CGTCGTATAAAACCCCCTTTAAGT 58.822 41.667 0.00 0.00 0.00 2.24
6401 6865 5.643348 CGTCGTATAAAACCCCCTTTAAGTT 59.357 40.000 0.00 0.00 0.00 2.66
6404 6868 6.430616 TCGTATAAAACCCCCTTTAAGTTGTG 59.569 38.462 0.00 0.00 0.00 3.33
6407 6871 2.463047 ACCCCCTTTAAGTTGTGCAA 57.537 45.000 0.00 0.00 0.00 4.08
6408 6872 2.036387 ACCCCCTTTAAGTTGTGCAAC 58.964 47.619 6.94 6.94 41.45 4.17
6423 6887 5.565592 TGTGCAACATCTTCCATGTAATC 57.434 39.130 0.00 0.00 45.67 1.75
6425 6889 3.953612 TGCAACATCTTCCATGTAATCCC 59.046 43.478 0.00 0.00 0.00 3.85
6427 6891 4.276926 GCAACATCTTCCATGTAATCCCTC 59.723 45.833 0.00 0.00 0.00 4.30
6428 6892 4.713792 ACATCTTCCATGTAATCCCTCC 57.286 45.455 0.00 0.00 0.00 4.30
6429 6893 3.071602 ACATCTTCCATGTAATCCCTCCG 59.928 47.826 0.00 0.00 0.00 4.63
6430 6894 2.759355 TCTTCCATGTAATCCCTCCGT 58.241 47.619 0.00 0.00 0.00 4.69
6431 6895 2.698797 TCTTCCATGTAATCCCTCCGTC 59.301 50.000 0.00 0.00 0.00 4.79
6432 6896 1.420430 TCCATGTAATCCCTCCGTCC 58.580 55.000 0.00 0.00 0.00 4.79
6433 6897 0.396811 CCATGTAATCCCTCCGTCCC 59.603 60.000 0.00 0.00 0.00 4.46
6435 6899 1.129058 ATGTAATCCCTCCGTCCCAC 58.871 55.000 0.00 0.00 0.00 4.61
6438 6902 1.489230 GTAATCCCTCCGTCCCACAAT 59.511 52.381 0.00 0.00 0.00 2.71
6439 6903 1.887797 AATCCCTCCGTCCCACAATA 58.112 50.000 0.00 0.00 0.00 1.90
6441 6905 2.779429 TCCCTCCGTCCCACAATATA 57.221 50.000 0.00 0.00 0.00 0.86
6442 6906 3.049108 TCCCTCCGTCCCACAATATAA 57.951 47.619 0.00 0.00 0.00 0.98
6443 6907 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
6447 6911 4.040461 CCTCCGTCCCACAATATAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
6449 6913 5.996644 TCCGTCCCACAATATAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
6450 6914 6.419791 TCCGTCCCACAATATAAGATGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
6451 6915 6.887545 TCCGTCCCACAATATAAGATGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
6452 6916 6.972328 CCGTCCCACAATATAAGATGTTTTTG 59.028 38.462 0.00 0.00 0.00 2.44
6792 7289 2.033208 GCCCACTACCCTCCGAACTAT 61.033 57.143 0.00 0.00 0.00 2.12
6837 7334 4.970611 CACTAGGATGTAGTGACGAATTCG 59.029 45.833 25.64 25.64 45.69 3.34
6950 7447 4.214119 GCTGTTCTCTGATGTGCTGTTTAA 59.786 41.667 0.00 0.00 0.00 1.52
7153 7654 5.120519 CGTGCATTTGACAATTATGGCTTTT 59.879 36.000 0.00 0.00 34.75 2.27
7246 7781 3.559238 AACATTGCTAGTTTCAAGCGG 57.441 42.857 0.00 0.00 43.11 5.52
7249 7784 3.568007 ACATTGCTAGTTTCAAGCGGAAA 59.432 39.130 2.94 2.94 43.11 3.13
7312 7855 8.565896 AACTTCATTGACACTATTATGCTGAA 57.434 30.769 0.00 0.00 0.00 3.02
7317 7860 8.959548 TCATTGACACTATTATGCTGAATTTGT 58.040 29.630 0.00 0.00 0.00 2.83
7467 8015 5.848286 TTGGTATCATGGGAGCATAAGAT 57.152 39.130 0.00 0.00 0.00 2.40
7499 8049 6.385176 TCACATGATATTCTCTCCACTCCTTT 59.615 38.462 0.00 0.00 0.00 3.11
7554 8104 4.283212 AGCTCTGGTATCTTAAGGCATCTC 59.717 45.833 1.85 0.00 0.00 2.75
7555 8105 4.283212 GCTCTGGTATCTTAAGGCATCTCT 59.717 45.833 1.85 0.00 0.00 3.10
7556 8106 5.478679 GCTCTGGTATCTTAAGGCATCTCTA 59.521 44.000 1.85 0.00 0.00 2.43
7557 8107 6.154363 GCTCTGGTATCTTAAGGCATCTCTAT 59.846 42.308 1.85 0.00 0.00 1.98
7558 8108 7.630513 GCTCTGGTATCTTAAGGCATCTCTATC 60.631 44.444 1.85 0.00 0.00 2.08
7559 8109 7.474445 TCTGGTATCTTAAGGCATCTCTATCT 58.526 38.462 1.85 0.00 0.00 1.98
7560 8110 7.952930 TCTGGTATCTTAAGGCATCTCTATCTT 59.047 37.037 1.85 0.00 0.00 2.40
7561 8111 9.249053 CTGGTATCTTAAGGCATCTCTATCTTA 57.751 37.037 1.85 0.00 0.00 2.10
7562 8112 9.601810 TGGTATCTTAAGGCATCTCTATCTTAA 57.398 33.333 1.85 0.00 32.76 1.85
7565 8115 6.998802 TCTTAAGGCATCTCTATCTTAAGGC 58.001 40.000 16.61 0.00 43.99 4.35
7566 8116 6.554982 TCTTAAGGCATCTCTATCTTAAGGCA 59.445 38.462 16.61 2.23 43.99 4.75
7567 8117 5.839517 AAGGCATCTCTATCTTAAGGCAT 57.160 39.130 1.85 0.00 0.00 4.40
7568 8118 5.419239 AGGCATCTCTATCTTAAGGCATC 57.581 43.478 1.85 0.00 0.00 3.91
7569 8119 5.092968 AGGCATCTCTATCTTAAGGCATCT 58.907 41.667 1.85 0.00 0.00 2.90
7570 8120 5.187576 AGGCATCTCTATCTTAAGGCATCTC 59.812 44.000 1.85 0.00 0.00 2.75
7571 8121 5.418676 GCATCTCTATCTTAAGGCATCTCC 58.581 45.833 1.85 0.00 0.00 3.71
7572 8122 5.046735 GCATCTCTATCTTAAGGCATCTCCA 60.047 44.000 1.85 0.00 37.29 3.86
7573 8123 6.519721 GCATCTCTATCTTAAGGCATCTCCAA 60.520 42.308 1.85 0.00 37.29 3.53
7581 8131 3.403936 GGCATCTCCAACGCCTATT 57.596 52.632 0.00 0.00 42.78 1.73
7582 8132 1.230324 GGCATCTCCAACGCCTATTC 58.770 55.000 0.00 0.00 42.78 1.75
7584 8134 2.565841 GCATCTCCAACGCCTATTCTT 58.434 47.619 0.00 0.00 0.00 2.52
7622 8172 3.963665 ACATGTTTTGTCATCCAACACG 58.036 40.909 0.00 0.00 36.69 4.49
7664 8214 3.936372 CGGCTCGGATAAAGAGGATAA 57.064 47.619 0.00 0.00 36.31 1.75
7665 8215 4.252971 CGGCTCGGATAAAGAGGATAAA 57.747 45.455 0.00 0.00 36.31 1.40
7666 8216 4.628074 CGGCTCGGATAAAGAGGATAAAA 58.372 43.478 0.00 0.00 36.31 1.52
7667 8217 5.054477 CGGCTCGGATAAAGAGGATAAAAA 58.946 41.667 0.00 0.00 36.31 1.94
7688 8238 5.913137 AAAAATGGATTTCCGACATAGCA 57.087 34.783 0.00 0.00 39.43 3.49
7689 8239 4.900635 AAATGGATTTCCGACATAGCAC 57.099 40.909 0.00 0.00 39.43 4.40
7690 8240 2.325583 TGGATTTCCGACATAGCACC 57.674 50.000 0.00 0.00 39.43 5.01
7691 8241 1.837439 TGGATTTCCGACATAGCACCT 59.163 47.619 0.00 0.00 39.43 4.00
7692 8242 2.213499 GGATTTCCGACATAGCACCTG 58.787 52.381 0.00 0.00 0.00 4.00
7693 8243 1.599542 GATTTCCGACATAGCACCTGC 59.400 52.381 0.00 0.00 42.49 4.85
7703 8253 2.124736 GCACCTGCGGCATTAGGA 60.125 61.111 13.08 0.00 37.52 2.94
7704 8254 1.526917 GCACCTGCGGCATTAGGAT 60.527 57.895 13.08 0.00 37.52 3.24
7705 8255 1.103398 GCACCTGCGGCATTAGGATT 61.103 55.000 13.08 0.00 37.52 3.01
7706 8256 0.947244 CACCTGCGGCATTAGGATTC 59.053 55.000 13.08 0.00 37.52 2.52
7707 8257 0.839946 ACCTGCGGCATTAGGATTCT 59.160 50.000 13.08 0.00 37.52 2.40
7708 8258 2.047061 ACCTGCGGCATTAGGATTCTA 58.953 47.619 13.08 0.00 37.52 2.10
7709 8259 2.438021 ACCTGCGGCATTAGGATTCTAA 59.562 45.455 13.08 0.00 39.51 2.10
7710 8260 3.070018 CCTGCGGCATTAGGATTCTAAG 58.930 50.000 1.75 0.00 38.69 2.18
7711 8261 3.244215 CCTGCGGCATTAGGATTCTAAGA 60.244 47.826 1.75 0.00 38.69 2.10
7712 8262 4.564406 CCTGCGGCATTAGGATTCTAAGAT 60.564 45.833 1.75 0.00 38.69 2.40
7713 8263 5.337571 CCTGCGGCATTAGGATTCTAAGATA 60.338 44.000 1.75 0.00 38.69 1.98
7714 8264 6.109156 TGCGGCATTAGGATTCTAAGATAA 57.891 37.500 0.00 0.00 38.69 1.75
7715 8265 6.711277 TGCGGCATTAGGATTCTAAGATAAT 58.289 36.000 0.00 0.00 38.69 1.28
7716 8266 7.168219 TGCGGCATTAGGATTCTAAGATAATT 58.832 34.615 0.00 0.00 38.69 1.40
7717 8267 7.665559 TGCGGCATTAGGATTCTAAGATAATTT 59.334 33.333 0.00 0.00 38.69 1.82
7718 8268 8.178313 GCGGCATTAGGATTCTAAGATAATTTC 58.822 37.037 0.00 0.00 38.69 2.17
7719 8269 9.442047 CGGCATTAGGATTCTAAGATAATTTCT 57.558 33.333 0.00 0.00 38.69 2.52
7724 8274 9.998106 TTAGGATTCTAAGATAATTTCTTCCCG 57.002 33.333 6.27 0.00 43.75 5.14
7725 8275 8.263854 AGGATTCTAAGATAATTTCTTCCCGA 57.736 34.615 6.27 1.95 43.75 5.14
7726 8276 8.714906 AGGATTCTAAGATAATTTCTTCCCGAA 58.285 33.333 6.27 8.14 43.75 4.30
7727 8277 9.338622 GGATTCTAAGATAATTTCTTCCCGAAA 57.661 33.333 6.27 0.00 43.75 3.46
7729 8279 9.907229 ATTCTAAGATAATTTCTTCCCGAAACT 57.093 29.630 6.27 0.00 43.75 2.66
7730 8280 9.734984 TTCTAAGATAATTTCTTCCCGAAACTT 57.265 29.630 6.27 0.00 43.75 2.66
7731 8281 9.379791 TCTAAGATAATTTCTTCCCGAAACTTC 57.620 33.333 6.27 0.00 43.75 3.01
7732 8282 7.392494 AAGATAATTTCTTCCCGAAACTTCC 57.608 36.000 0.00 0.00 43.90 3.46
7733 8283 5.886474 AGATAATTTCTTCCCGAAACTTCCC 59.114 40.000 0.00 0.00 43.90 3.97
7734 8284 3.518992 ATTTCTTCCCGAAACTTCCCA 57.481 42.857 0.00 0.00 43.90 4.37
7735 8285 3.300239 TTTCTTCCCGAAACTTCCCAA 57.700 42.857 0.00 0.00 36.72 4.12
7736 8286 2.561478 TCTTCCCGAAACTTCCCAAG 57.439 50.000 0.00 0.00 0.00 3.61
7737 8287 2.051692 TCTTCCCGAAACTTCCCAAGA 58.948 47.619 0.00 0.00 0.00 3.02
7738 8288 2.440253 TCTTCCCGAAACTTCCCAAGAA 59.560 45.455 0.00 0.00 0.00 2.52
7739 8289 3.117813 TCTTCCCGAAACTTCCCAAGAAA 60.118 43.478 0.00 0.00 0.00 2.52
7740 8290 3.300239 TCCCGAAACTTCCCAAGAAAA 57.700 42.857 0.00 0.00 0.00 2.29
7741 8291 3.633418 TCCCGAAACTTCCCAAGAAAAA 58.367 40.909 0.00 0.00 0.00 1.94
7742 8292 4.219919 TCCCGAAACTTCCCAAGAAAAAT 58.780 39.130 0.00 0.00 0.00 1.82
7743 8293 4.279922 TCCCGAAACTTCCCAAGAAAAATC 59.720 41.667 0.00 0.00 0.00 2.17
7744 8294 4.556233 CCGAAACTTCCCAAGAAAAATCC 58.444 43.478 0.00 0.00 0.00 3.01
7745 8295 4.556233 CGAAACTTCCCAAGAAAAATCCC 58.444 43.478 0.00 0.00 0.00 3.85
7746 8296 4.560716 CGAAACTTCCCAAGAAAAATCCCC 60.561 45.833 0.00 0.00 0.00 4.81
7747 8297 3.923273 ACTTCCCAAGAAAAATCCCCT 57.077 42.857 0.00 0.00 0.00 4.79
7748 8298 4.213531 ACTTCCCAAGAAAAATCCCCTT 57.786 40.909 0.00 0.00 0.00 3.95
7749 8299 3.903714 ACTTCCCAAGAAAAATCCCCTTG 59.096 43.478 0.00 0.00 37.58 3.61
7750 8300 3.628832 TCCCAAGAAAAATCCCCTTGT 57.371 42.857 0.00 0.00 36.47 3.16
7751 8301 3.238597 TCCCAAGAAAAATCCCCTTGTG 58.761 45.455 0.00 0.00 36.47 3.33
7752 8302 2.972021 CCCAAGAAAAATCCCCTTGTGT 59.028 45.455 0.00 0.00 36.47 3.72
7753 8303 3.006859 CCCAAGAAAAATCCCCTTGTGTC 59.993 47.826 0.00 0.00 36.47 3.67
7754 8304 3.640967 CCAAGAAAAATCCCCTTGTGTCA 59.359 43.478 0.00 0.00 36.47 3.58
7755 8305 4.100808 CCAAGAAAAATCCCCTTGTGTCAA 59.899 41.667 0.00 0.00 36.47 3.18
7756 8306 5.396213 CCAAGAAAAATCCCCTTGTGTCAAA 60.396 40.000 0.00 0.00 36.47 2.69
7757 8307 5.948742 AGAAAAATCCCCTTGTGTCAAAA 57.051 34.783 0.00 0.00 0.00 2.44
7758 8308 6.306643 AGAAAAATCCCCTTGTGTCAAAAA 57.693 33.333 0.00 0.00 0.00 1.94
7786 8336 8.429237 AAAATGGTTAAGGATACAATCAACCA 57.571 30.769 6.46 6.46 46.73 3.67
7787 8337 8.429237 AAATGGTTAAGGATACAATCAACCAA 57.571 30.769 7.96 0.00 46.05 3.67
7788 8338 8.608185 AATGGTTAAGGATACAATCAACCAAT 57.392 30.769 7.96 0.00 46.05 3.16
7789 8339 9.707957 AATGGTTAAGGATACAATCAACCAATA 57.292 29.630 7.96 0.00 46.05 1.90
7790 8340 9.707957 ATGGTTAAGGATACAATCAACCAATAA 57.292 29.630 7.96 0.00 46.05 1.40
7791 8341 9.535170 TGGTTAAGGATACAATCAACCAATAAA 57.465 29.630 1.66 0.00 41.70 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.633921 CCTCTCCCTCCTTCTCCTCA 59.366 60.000 0.00 0.00 0.00 3.86
90 91 0.341609 CCTTCCTCCTCTCCCTCCTT 59.658 60.000 0.00 0.00 0.00 3.36
160 161 2.418910 CGCGTCATCTCCCACCTCT 61.419 63.158 0.00 0.00 0.00 3.69
248 256 2.631545 AGTAGTGCCCGAGTTGTTTAGT 59.368 45.455 0.00 0.00 0.00 2.24
307 320 1.406970 GGCTTTTCGCGTCTCTCTCG 61.407 60.000 5.77 0.00 40.44 4.04
314 327 2.126850 GCCTTGGCTTTTCGCGTC 60.127 61.111 5.77 0.00 40.44 5.19
579 606 0.468226 GAGCGAGAGGGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
582 609 2.542907 GCGAGCGAGAGGGAGAGAG 61.543 68.421 0.00 0.00 0.00 3.20
583 610 2.515057 GCGAGCGAGAGGGAGAGA 60.515 66.667 0.00 0.00 0.00 3.10
601 628 2.590114 GGGTTACGGGTGGCAGAGT 61.590 63.158 0.00 0.00 0.00 3.24
806 880 2.842462 ATAGGCCGCGGATCCACA 60.842 61.111 33.48 13.79 0.00 4.17
808 882 2.842462 ACATAGGCCGCGGATCCA 60.842 61.111 33.48 10.84 0.00 3.41
822 896 3.118956 GCTCTACACCTCACTAAGCACAT 60.119 47.826 0.00 0.00 0.00 3.21
881 956 4.711949 CTTGCACGGGCCAGAGCT 62.712 66.667 23.84 0.00 40.13 4.09
900 975 2.555199 CTAGCCACAGCATCACCTAAC 58.445 52.381 0.00 0.00 43.56 2.34
1185 1260 1.555075 CTCGGGTTCCCAGATTCTTCA 59.445 52.381 8.70 0.00 0.00 3.02
1522 1600 7.757526 TGAAAACCGTGATAATAACAATCCAG 58.242 34.615 0.00 0.00 0.00 3.86
1540 1618 5.465724 CAGACCTACAACACTACTGAAAACC 59.534 44.000 0.00 0.00 0.00 3.27
1643 1721 5.874810 TCTGCATCGTTCTATTAAAGCAACT 59.125 36.000 0.00 0.00 0.00 3.16
1680 1759 5.981088 AAACAGATCACCATTATGCAACA 57.019 34.783 0.00 0.00 0.00 3.33
1772 1851 9.733556 TCAACACAGAATATAATTGTAAGGTGT 57.266 29.630 0.00 0.00 37.35 4.16
1811 1890 6.833041 TCTGATAACCCGGCAAATAAGAATA 58.167 36.000 0.00 0.00 0.00 1.75
1822 1901 2.093658 TCTGAACTTCTGATAACCCGGC 60.094 50.000 0.00 0.00 0.00 6.13
1845 1924 6.094742 ACATCAAGACAACACATACACAAACA 59.905 34.615 0.00 0.00 0.00 2.83
1856 1935 6.102663 AGTCTATAGCACATCAAGACAACAC 58.897 40.000 0.00 0.00 39.20 3.32
2214 2295 9.478238 TCTTTGATGATCCAATCTTCCAAATTA 57.522 29.630 0.00 0.00 33.78 1.40
2296 2378 7.402054 CCATTCCATATATAAGCAGGTGGTTA 58.598 38.462 4.21 4.21 41.48 2.85
2339 2421 1.896220 CTTGCTCCTTGCTGGTTGTA 58.104 50.000 0.00 0.00 43.37 2.41
2340 2422 1.458639 GCTTGCTCCTTGCTGGTTGT 61.459 55.000 0.00 0.00 43.37 3.32
2462 2544 8.034058 AGTATTTCAGAGTGCAACAATTACTC 57.966 34.615 0.00 0.00 41.43 2.59
2552 2635 7.376072 GCTCGCTACAATTTTGACAATTATACC 59.624 37.037 0.00 0.00 0.00 2.73
2569 2652 4.672587 ATAAATCTGGAAGCTCGCTACA 57.327 40.909 0.00 0.00 0.00 2.74
2570 2653 5.050490 TGAATAAATCTGGAAGCTCGCTAC 58.950 41.667 0.00 0.00 0.00 3.58
2575 2658 6.512415 CGGTTCATGAATAAATCTGGAAGCTC 60.512 42.308 12.12 0.00 37.26 4.09
2769 2864 6.620678 TCTATGGATAGTTTGCTTGTTTTGC 58.379 36.000 0.00 0.00 0.00 3.68
3180 3281 1.237285 ACTTGCTGTTGACGGGCATC 61.237 55.000 0.00 0.00 35.84 3.91
3318 3419 5.022787 CCCAGAAATTTCCCATCCAACTTA 58.977 41.667 14.61 0.00 0.00 2.24
3319 3420 3.840078 CCCAGAAATTTCCCATCCAACTT 59.160 43.478 14.61 0.00 0.00 2.66
3456 3720 8.514594 TGAAACTGCCAATTAAAGTAATCAGAG 58.485 33.333 0.00 0.00 0.00 3.35
3625 3974 7.667219 TGGGCAGATTTTAGAATATCAATCCTC 59.333 37.037 0.00 0.00 0.00 3.71
3815 4165 8.424918 AGGATAAGCATATATTTCCATCCTACG 58.575 37.037 11.45 0.00 39.34 3.51
3990 4341 1.134159 AGTGCATCTGGCTCATCCTTC 60.134 52.381 0.00 0.00 45.15 3.46
4011 4362 1.001020 ATCAATGGCTGGCGGAACA 60.001 52.632 0.00 0.00 0.00 3.18
4537 4922 2.223947 ACTGTACACGCACAATCAGTCA 60.224 45.455 0.00 0.00 31.81 3.41
4613 4998 5.590259 AGAATCAATACACGAGGAAAATGGG 59.410 40.000 0.00 0.00 0.00 4.00
4682 5103 1.708341 AGGGCAAGCTTTTGTCATGT 58.292 45.000 0.00 0.00 0.00 3.21
4711 5132 3.285484 CATCTACCAGCCAGCAGAATTT 58.715 45.455 0.00 0.00 0.00 1.82
4885 5309 2.741145 ACAACAACAAAGCCTGGGTAA 58.259 42.857 0.00 0.00 0.00 2.85
5112 5573 6.822667 ACAACTCTGTCATCATTTAATGCA 57.177 33.333 0.00 0.00 0.00 3.96
5268 5729 8.203485 TGGATACTTCTTTCAAGCAAACAATTT 58.797 29.630 0.00 0.00 37.61 1.82
5586 6047 2.957402 AACTTGAGAAGACCCATGCA 57.043 45.000 0.00 0.00 0.00 3.96
6111 6574 3.380004 TGGTATAATTTTTGCTCCTGCCG 59.620 43.478 0.00 0.00 38.71 5.69
6125 6588 6.049149 CAGTCGGTCAATTCAGTGGTATAAT 58.951 40.000 0.00 0.00 0.00 1.28
6180 6643 9.912634 ACTGAATTCACAAAAATTATACCACTG 57.087 29.630 3.38 0.00 0.00 3.66
6181 6644 9.912634 CACTGAATTCACAAAAATTATACCACT 57.087 29.630 3.38 0.00 0.00 4.00
6182 6645 9.139174 CCACTGAATTCACAAAAATTATACCAC 57.861 33.333 3.38 0.00 0.00 4.16
6183 6646 8.865090 ACCACTGAATTCACAAAAATTATACCA 58.135 29.630 3.38 0.00 0.00 3.25
6194 6657 9.202273 GCAAAAATTATACCACTGAATTCACAA 57.798 29.630 3.38 0.00 0.00 3.33
6195 6658 8.584157 AGCAAAAATTATACCACTGAATTCACA 58.416 29.630 3.38 0.00 0.00 3.58
6196 6659 8.986477 AGCAAAAATTATACCACTGAATTCAC 57.014 30.769 3.38 0.00 0.00 3.18
6197 6660 8.250332 GGAGCAAAAATTATACCACTGAATTCA 58.750 33.333 8.12 8.12 0.00 2.57
6381 6845 6.015265 TGCACAACTTAAAGGGGGTTTTATAC 60.015 38.462 0.00 0.00 0.00 1.47
6386 6850 2.753247 TGCACAACTTAAAGGGGGTTT 58.247 42.857 0.00 0.00 0.00 3.27
6387 6851 2.432874 GTTGCACAACTTAAAGGGGGTT 59.567 45.455 6.27 0.00 38.25 4.11
6388 6852 2.036387 GTTGCACAACTTAAAGGGGGT 58.964 47.619 6.27 0.00 38.25 4.95
6389 6853 2.035632 TGTTGCACAACTTAAAGGGGG 58.964 47.619 14.16 0.00 41.67 5.40
6390 6854 3.573967 AGATGTTGCACAACTTAAAGGGG 59.426 43.478 14.16 0.00 41.67 4.79
6391 6855 4.853924 AGATGTTGCACAACTTAAAGGG 57.146 40.909 14.16 0.00 41.67 3.95
6392 6856 5.221224 TGGAAGATGTTGCACAACTTAAAGG 60.221 40.000 14.16 0.00 40.59 3.11
6393 6857 5.830912 TGGAAGATGTTGCACAACTTAAAG 58.169 37.500 14.16 0.00 40.59 1.85
6394 6858 5.843673 TGGAAGATGTTGCACAACTTAAA 57.156 34.783 14.16 0.00 40.59 1.52
6395 6859 5.301551 ACATGGAAGATGTTGCACAACTTAA 59.698 36.000 14.16 0.00 40.59 1.85
6396 6860 4.826733 ACATGGAAGATGTTGCACAACTTA 59.173 37.500 14.16 0.00 40.59 2.24
6398 6862 3.225104 ACATGGAAGATGTTGCACAACT 58.775 40.909 14.16 0.84 41.67 3.16
6400 6864 5.105797 GGATTACATGGAAGATGTTGCACAA 60.106 40.000 0.00 0.00 36.75 3.33
6401 6865 4.398988 GGATTACATGGAAGATGTTGCACA 59.601 41.667 0.00 0.00 36.75 4.57
6404 6868 4.210331 AGGGATTACATGGAAGATGTTGC 58.790 43.478 0.00 0.00 33.76 4.17
6407 6871 3.071602 CGGAGGGATTACATGGAAGATGT 59.928 47.826 0.00 0.00 36.13 3.06
6408 6872 3.071602 ACGGAGGGATTACATGGAAGATG 59.928 47.826 0.00 0.00 0.00 2.90
6409 6873 3.318313 ACGGAGGGATTACATGGAAGAT 58.682 45.455 0.00 0.00 0.00 2.40
6410 6874 2.698797 GACGGAGGGATTACATGGAAGA 59.301 50.000 0.00 0.00 0.00 2.87
6411 6875 2.224305 GGACGGAGGGATTACATGGAAG 60.224 54.545 0.00 0.00 0.00 3.46
6412 6876 1.766496 GGACGGAGGGATTACATGGAA 59.234 52.381 0.00 0.00 0.00 3.53
6413 6877 1.420430 GGACGGAGGGATTACATGGA 58.580 55.000 0.00 0.00 0.00 3.41
6414 6878 0.396811 GGGACGGAGGGATTACATGG 59.603 60.000 0.00 0.00 0.00 3.66
6415 6879 1.128200 TGGGACGGAGGGATTACATG 58.872 55.000 0.00 0.00 0.00 3.21
6416 6880 1.129058 GTGGGACGGAGGGATTACAT 58.871 55.000 0.00 0.00 0.00 2.29
6419 6883 1.887797 ATTGTGGGACGGAGGGATTA 58.112 50.000 0.00 0.00 0.00 1.75
6421 6885 2.118403 ATATTGTGGGACGGAGGGAT 57.882 50.000 0.00 0.00 0.00 3.85
6422 6886 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
6423 6887 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
6425 6889 5.215252 ACATCTTATATTGTGGGACGGAG 57.785 43.478 0.00 0.00 0.00 4.63
6427 6891 6.693315 AAAACATCTTATATTGTGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
6428 6892 6.472163 GCAAAAACATCTTATATTGTGGGACG 59.528 38.462 0.00 0.00 0.00 4.79
6429 6893 7.319646 TGCAAAAACATCTTATATTGTGGGAC 58.680 34.615 0.00 0.00 0.00 4.46
6430 6894 7.473735 TGCAAAAACATCTTATATTGTGGGA 57.526 32.000 0.00 0.00 0.00 4.37
6431 6895 7.225145 CCATGCAAAAACATCTTATATTGTGGG 59.775 37.037 0.00 0.00 0.00 4.61
6432 6896 7.980662 TCCATGCAAAAACATCTTATATTGTGG 59.019 33.333 0.00 0.00 0.00 4.17
6433 6897 8.929827 TCCATGCAAAAACATCTTATATTGTG 57.070 30.769 0.00 0.00 0.00 3.33
6774 7271 1.687123 CCATAGTTCGGAGGGTAGTGG 59.313 57.143 0.00 0.00 0.00 4.00
6792 7289 2.543037 TCATGTCCAGCTAGTACCCA 57.457 50.000 0.00 0.00 0.00 4.51
6837 7334 0.249280 CAGGCCGAACAACAAAACCC 60.249 55.000 0.00 0.00 0.00 4.11
7242 7777 4.760204 AGTTAAACTAGCAATGTTTCCGCT 59.240 37.500 5.28 0.00 38.41 5.52
7243 7778 5.043189 AGTTAAACTAGCAATGTTTCCGC 57.957 39.130 5.28 0.00 38.41 5.54
7244 7779 8.197988 AGATAGTTAAACTAGCAATGTTTCCG 57.802 34.615 0.00 0.00 39.41 4.30
7249 7784 9.587772 CAGTGTAGATAGTTAAACTAGCAATGT 57.412 33.333 0.00 0.00 39.41 2.71
7271 7814 9.681692 TCAATGAAGTTAAAATCATGAACAGTG 57.318 29.630 0.00 0.00 36.44 3.66
7292 7835 9.229784 GACAAATTCAGCATAATAGTGTCAATG 57.770 33.333 15.55 0.00 35.78 2.82
7430 7978 9.439500 CCATGATACCAATTTCAAAAAGTGAAT 57.561 29.630 0.00 0.00 45.71 2.57
7448 7996 6.893583 ACCATATCTTATGCTCCCATGATAC 58.106 40.000 0.00 0.00 32.85 2.24
7467 8015 8.753133 GTGGAGAGAATATCATGTGATACCATA 58.247 37.037 4.93 0.00 39.57 2.74
7499 8049 4.616671 TCATGGGTTGGGGATTTTATCA 57.383 40.909 0.00 0.00 0.00 2.15
7554 8104 3.743396 GCGTTGGAGATGCCTTAAGATAG 59.257 47.826 3.36 0.00 37.63 2.08
7555 8105 3.728845 GCGTTGGAGATGCCTTAAGATA 58.271 45.455 3.36 0.00 37.63 1.98
7556 8106 2.565841 GCGTTGGAGATGCCTTAAGAT 58.434 47.619 3.36 0.00 37.63 2.40
7557 8107 2.024176 GCGTTGGAGATGCCTTAAGA 57.976 50.000 3.36 0.00 37.63 2.10
7564 8114 2.246719 AGAATAGGCGTTGGAGATGC 57.753 50.000 0.00 0.00 39.65 3.91
7565 8115 4.310769 CCTAAGAATAGGCGTTGGAGATG 58.689 47.826 0.00 0.00 42.28 2.90
7566 8116 4.608948 CCTAAGAATAGGCGTTGGAGAT 57.391 45.455 0.00 0.00 42.28 2.75
7578 8128 8.185506 TGTCTAACAACACAGTCCTAAGAATA 57.814 34.615 0.00 0.00 0.00 1.75
7581 8131 6.041637 ACATGTCTAACAACACAGTCCTAAGA 59.958 38.462 0.00 0.00 30.55 2.10
7582 8132 6.223852 ACATGTCTAACAACACAGTCCTAAG 58.776 40.000 0.00 0.00 30.55 2.18
7584 8134 5.801531 ACATGTCTAACAACACAGTCCTA 57.198 39.130 0.00 0.00 30.55 2.94
7622 8172 3.181494 GGTTGGCAAACCGATACATAACC 60.181 47.826 7.40 0.00 46.32 2.85
7644 8194 3.936372 TTATCCTCTTTATCCGAGCCG 57.064 47.619 0.00 0.00 0.00 5.52
7666 8216 5.394115 GGTGCTATGTCGGAAATCCATTTTT 60.394 40.000 0.00 0.00 35.14 1.94
7667 8217 4.097892 GGTGCTATGTCGGAAATCCATTTT 59.902 41.667 0.00 0.00 35.14 1.82
7668 8218 3.632145 GGTGCTATGTCGGAAATCCATTT 59.368 43.478 0.00 0.00 35.14 2.32
7669 8219 3.117888 AGGTGCTATGTCGGAAATCCATT 60.118 43.478 0.00 0.00 35.14 3.16
7670 8220 2.439507 AGGTGCTATGTCGGAAATCCAT 59.560 45.455 0.00 0.00 35.14 3.41
7671 8221 1.837439 AGGTGCTATGTCGGAAATCCA 59.163 47.619 0.00 0.00 35.14 3.41
7672 8222 2.213499 CAGGTGCTATGTCGGAAATCC 58.787 52.381 0.00 0.00 0.00 3.01
7673 8223 1.599542 GCAGGTGCTATGTCGGAAATC 59.400 52.381 0.00 0.00 38.21 2.17
7674 8224 1.668419 GCAGGTGCTATGTCGGAAAT 58.332 50.000 0.00 0.00 38.21 2.17
7675 8225 0.739462 CGCAGGTGCTATGTCGGAAA 60.739 55.000 0.00 0.00 39.32 3.13
7676 8226 1.153647 CGCAGGTGCTATGTCGGAA 60.154 57.895 0.00 0.00 39.32 4.30
7677 8227 2.494445 CGCAGGTGCTATGTCGGA 59.506 61.111 0.00 0.00 39.32 4.55
7687 8237 3.744214 TTAGAATCCTAATGCCGCAGGTG 60.744 47.826 0.00 0.00 38.96 4.00
7688 8238 2.438021 TTAGAATCCTAATGCCGCAGGT 59.562 45.455 0.00 0.00 38.96 4.00
7689 8239 3.070018 CTTAGAATCCTAATGCCGCAGG 58.930 50.000 0.00 0.00 41.86 4.85
7690 8240 3.995199 TCTTAGAATCCTAATGCCGCAG 58.005 45.455 0.00 0.00 34.62 5.18
7691 8241 4.623932 ATCTTAGAATCCTAATGCCGCA 57.376 40.909 0.00 0.00 34.62 5.69
7692 8242 7.617041 AATTATCTTAGAATCCTAATGCCGC 57.383 36.000 0.00 0.00 34.62 6.53
7693 8243 9.442047 AGAAATTATCTTAGAATCCTAATGCCG 57.558 33.333 0.00 0.00 33.39 5.69
7715 8265 3.117813 TCTTGGGAAGTTTCGGGAAGAAA 60.118 43.478 0.00 0.00 45.76 2.52
7716 8266 2.440253 TCTTGGGAAGTTTCGGGAAGAA 59.560 45.455 0.00 0.00 37.01 2.52
7717 8267 2.051692 TCTTGGGAAGTTTCGGGAAGA 58.948 47.619 0.00 0.00 0.00 2.87
7718 8268 2.561478 TCTTGGGAAGTTTCGGGAAG 57.439 50.000 0.00 0.00 0.00 3.46
7719 8269 3.300239 TTTCTTGGGAAGTTTCGGGAA 57.700 42.857 0.00 0.00 32.61 3.97
7720 8270 3.300239 TTTTCTTGGGAAGTTTCGGGA 57.700 42.857 0.00 0.00 32.61 5.14
7721 8271 4.556233 GATTTTTCTTGGGAAGTTTCGGG 58.444 43.478 0.00 0.00 32.61 5.14
7722 8272 4.556233 GGATTTTTCTTGGGAAGTTTCGG 58.444 43.478 0.00 0.00 32.61 4.30
7723 8273 4.556233 GGGATTTTTCTTGGGAAGTTTCG 58.444 43.478 0.00 0.00 32.61 3.46
7724 8274 4.593206 AGGGGATTTTTCTTGGGAAGTTTC 59.407 41.667 0.00 0.00 32.61 2.78
7725 8275 4.566837 AGGGGATTTTTCTTGGGAAGTTT 58.433 39.130 0.00 0.00 32.61 2.66
7726 8276 4.213531 AGGGGATTTTTCTTGGGAAGTT 57.786 40.909 0.00 0.00 32.61 2.66
7727 8277 3.903714 CAAGGGGATTTTTCTTGGGAAGT 59.096 43.478 0.00 0.00 35.53 3.01
7728 8278 3.903714 ACAAGGGGATTTTTCTTGGGAAG 59.096 43.478 0.00 0.00 41.35 3.46
7729 8279 3.645687 CACAAGGGGATTTTTCTTGGGAA 59.354 43.478 0.00 0.00 42.65 3.97
7730 8280 3.238597 CACAAGGGGATTTTTCTTGGGA 58.761 45.455 0.00 0.00 42.65 4.37
7731 8281 2.972021 ACACAAGGGGATTTTTCTTGGG 59.028 45.455 0.00 0.00 44.76 4.12
7732 8282 3.640967 TGACACAAGGGGATTTTTCTTGG 59.359 43.478 0.00 0.00 41.35 3.61
7733 8283 4.935352 TGACACAAGGGGATTTTTCTTG 57.065 40.909 0.00 0.00 42.37 3.02
7734 8284 5.948742 TTTGACACAAGGGGATTTTTCTT 57.051 34.783 0.00 0.00 0.00 2.52
7735 8285 5.948742 TTTTGACACAAGGGGATTTTTCT 57.051 34.783 0.00 0.00 0.00 2.52
7760 8310 8.875168 TGGTTGATTGTATCCTTAACCATTTTT 58.125 29.630 0.00 0.00 41.68 1.94
7761 8311 8.429237 TGGTTGATTGTATCCTTAACCATTTT 57.571 30.769 0.00 0.00 41.68 1.82
7762 8312 8.429237 TTGGTTGATTGTATCCTTAACCATTT 57.571 30.769 7.39 0.00 44.73 2.32
7763 8313 8.608185 ATTGGTTGATTGTATCCTTAACCATT 57.392 30.769 7.39 2.27 44.73 3.16
7764 8314 9.707957 TTATTGGTTGATTGTATCCTTAACCAT 57.292 29.630 7.39 2.18 44.73 3.55
7765 8315 9.535170 TTTATTGGTTGATTGTATCCTTAACCA 57.465 29.630 0.00 0.00 43.99 3.67


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

AutoCloner maintained by Alex Coulton.