Multiple sequence alignment - TraesCS6D01G344000

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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 TraesCS6D01G344000 chr6D 100.000 5030 0 0 1 5030 443851026 443845997 0.000000e+00 9289.0
1 TraesCS6D01G344000 chr6D 82.162 185 23 5 163 337 388209745 388209929 3.140000e-32 150.0
2 TraesCS6D01G344000 chr6D 83.916 143 22 1 159 301 419484637 419484778 8.780000e-28 135.0
3 TraesCS6D01G344000 chr6B 92.840 4567 183 65 104 4592 668251575 668247075 0.000000e+00 6490.0
4 TraesCS6D01G344000 chr6B 90.152 264 19 4 4707 4966 668246847 668246587 2.240000e-88 337.0
5 TraesCS6D01G344000 chr6B 83.750 80 5 6 4424 4500 278127864 278127790 9.040000e-08 69.4
6 TraesCS6D01G344000 chr6A 94.048 4234 105 50 411 4592 591440650 591436512 0.000000e+00 6287.0
7 TraesCS6D01G344000 chr6A 91.753 970 46 20 3565 4515 591436502 591435548 0.000000e+00 1317.0
8 TraesCS6D01G344000 chr6A 91.985 262 15 2 4255 4515 591435547 591435291 3.700000e-96 363.0
9 TraesCS6D01G344000 chr6A 93.367 196 12 1 4835 5030 591429603 591429409 6.370000e-74 289.0
10 TraesCS6D01G344000 chr6A 79.947 379 25 18 4485 4824 591431257 591430891 1.090000e-56 231.0
11 TraesCS6D01G344000 chr6A 95.385 130 5 1 4253 4381 591431385 591431256 6.600000e-49 206.0
12 TraesCS6D01G344000 chr7D 90.595 2169 186 18 1059 3218 93791680 93789521 0.000000e+00 2859.0
13 TraesCS6D01G344000 chr7D 85.506 1511 193 25 1719 3219 606636159 606637653 0.000000e+00 1554.0
14 TraesCS6D01G344000 chr7D 87.017 362 45 2 3305 3665 93789522 93789162 1.690000e-109 407.0
15 TraesCS6D01G344000 chr7D 83.385 325 50 4 3325 3647 606637781 606638103 1.060000e-76 298.0
16 TraesCS6D01G344000 chr7D 80.000 290 44 8 3744 4032 93789060 93788784 8.540000e-48 202.0
17 TraesCS6D01G344000 chr7D 85.621 153 16 4 3882 4031 606638255 606638404 6.740000e-34 156.0
18 TraesCS6D01G344000 chr7D 93.069 101 7 0 5 105 64732052 64732152 1.130000e-31 148.0
19 TraesCS6D01G344000 chr7A 90.498 2168 190 16 1059 3218 96570516 96568357 0.000000e+00 2848.0
20 TraesCS6D01G344000 chr7A 86.406 1486 178 21 1712 3188 698679382 698677912 0.000000e+00 1604.0
21 TraesCS6D01G344000 chr7A 87.569 362 43 2 3305 3665 96568358 96567998 7.790000e-113 418.0
22 TraesCS6D01G344000 chr7A 85.294 306 43 2 3343 3647 698677728 698677424 1.050000e-81 315.0
23 TraesCS6D01G344000 chr7A 81.315 289 42 8 3744 4032 96567893 96567617 1.820000e-54 224.0
24 TraesCS6D01G344000 chr7A 86.897 145 17 2 3888 4031 698677266 698677123 1.450000e-35 161.0
25 TraesCS6D01G344000 chr7A 80.282 142 24 3 162 301 690204429 690204290 2.480000e-18 104.0
26 TraesCS6D01G344000 chr7B 89.627 2169 207 18 1059 3218 47003652 47001493 0.000000e+00 2743.0
27 TraesCS6D01G344000 chr7B 85.894 1510 193 18 1717 3219 690754917 690753421 0.000000e+00 1591.0
28 TraesCS6D01G344000 chr7B 88.406 552 58 6 1168 1716 690755575 690755027 0.000000e+00 660.0
29 TraesCS6D01G344000 chr7B 87.569 362 43 2 3305 3665 47001494 47001134 7.790000e-113 418.0
30 TraesCS6D01G344000 chr7B 89.850 266 21 3 4704 4966 620326058 620326320 2.240000e-88 337.0
31 TraesCS6D01G344000 chr7B 85.246 305 45 0 3343 3647 690753260 690752956 1.050000e-81 315.0
32 TraesCS6D01G344000 chr7B 80.969 289 43 8 3744 4032 47001007 47000731 8.480000e-53 219.0
33 TraesCS6D01G344000 chr7B 86.806 144 17 2 3890 4032 690752796 690752654 5.210000e-35 159.0
34 TraesCS6D01G344000 chr7B 93.069 101 7 0 5 105 383714637 383714737 1.130000e-31 148.0
35 TraesCS6D01G344000 chr1D 82.609 1794 281 27 1168 2941 349794639 349792857 0.000000e+00 1555.0
36 TraesCS6D01G344000 chr1D 78.363 171 34 2 165 335 462475955 462476122 1.910000e-19 108.0
37 TraesCS6D01G344000 chr1B 82.320 1793 288 25 1168 2941 471763387 471761605 0.000000e+00 1528.0
38 TraesCS6D01G344000 chr1B 94.545 110 6 0 1 110 502961256 502961365 2.410000e-38 171.0
39 TraesCS6D01G344000 chr1B 93.204 103 7 0 1 103 430155412 430155514 8.720000e-33 152.0
40 TraesCS6D01G344000 chr1A 82.245 1791 293 22 1168 2941 450096395 450094613 0.000000e+00 1522.0
41 TraesCS6D01G344000 chr4B 81.015 532 81 16 2425 2940 586467254 586466727 6.060000e-109 405.0
42 TraesCS6D01G344000 chr4B 95.238 105 5 0 1 105 360898099 360898203 3.110000e-37 167.0
43 TraesCS6D01G344000 chr4B 86.765 136 13 5 162 294 619938348 619938481 4.060000e-31 147.0
44 TraesCS6D01G344000 chr4B 79.137 139 13 5 206 335 659479773 659479904 1.160000e-11 82.4
45 TraesCS6D01G344000 chr2A 88.024 334 22 10 560 887 348213529 348213208 3.680000e-101 379.0
46 TraesCS6D01G344000 chr2A 82.759 116 9 5 4374 4484 252088180 252088289 5.360000e-15 93.5
47 TraesCS6D01G344000 chr5B 89.850 266 21 3 4704 4966 633625296 633625558 2.240000e-88 337.0
48 TraesCS6D01G344000 chr3B 93.396 106 7 0 1 106 649645654 649645759 1.870000e-34 158.0
49 TraesCS6D01G344000 chr3B 91.429 105 9 0 1 105 750228575 750228679 1.460000e-30 145.0
50 TraesCS6D01G344000 chr3B 80.420 143 21 6 162 301 451404848 451404710 8.910000e-18 102.0
51 TraesCS6D01G344000 chr3B 85.915 71 4 2 4418 4488 443358074 443358138 2.510000e-08 71.3
52 TraesCS6D01G344000 chr2B 93.069 101 7 0 5 105 52463318 52463218 1.130000e-31 148.0
53 TraesCS6D01G344000 chr2B 96.875 32 1 0 304 335 793485665 793485696 3.000000e-03 54.7
54 TraesCS6D01G344000 chr5A 91.589 107 7 2 1 105 480561113 480561007 4.060000e-31 147.0
55 TraesCS6D01G344000 chr4D 85.507 138 19 1 163 300 504223913 504223777 5.250000e-30 143.0
56 TraesCS6D01G344000 chr2D 85.000 140 20 1 162 301 82141344 82141206 1.890000e-29 141.0
57 TraesCS6D01G344000 chr2D 85.417 96 8 4 4374 4464 256675487 256675393 1.490000e-15 95.3
58 TraesCS6D01G344000 chr2D 84.270 89 12 2 4377 4464 619479371 619479458 8.970000e-13 86.1
59 TraesCS6D01G344000 chr3A 79.429 175 24 8 163 336 304768625 304768788 4.120000e-21 113.0
60 TraesCS6D01G344000 chr3A 79.866 149 19 4 201 338 507621476 507621624 1.150000e-16 99.0
61 TraesCS6D01G344000 chr3A 85.714 91 9 1 4378 4464 456381680 456381770 5.360000e-15 93.5
62 TraesCS6D01G344000 chr3D 87.234 94 5 2 4378 4464 94644757 94644850 3.200000e-17 100.0
63 TraesCS6D01G344000 chr3D 82.500 120 13 5 163 282 516076149 516076038 1.150000e-16 99.0
64 TraesCS6D01G344000 chr4A 96.970 33 1 0 305 337 108768385 108768417 7.030000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G344000 chr6D 443845997 443851026 5029 True 9289.000000 9289 100.000000 1 5030 1 chr6D.!!$R1 5029
1 TraesCS6D01G344000 chr6B 668246587 668251575 4988 True 3413.500000 6490 91.496000 104 4966 2 chr6B.!!$R2 4862
2 TraesCS6D01G344000 chr6A 591429409 591440650 11241 True 1448.833333 6287 91.080833 411 5030 6 chr6A.!!$R1 4619
3 TraesCS6D01G344000 chr7D 93788784 93791680 2896 True 1156.000000 2859 85.870667 1059 4032 3 chr7D.!!$R1 2973
4 TraesCS6D01G344000 chr7D 606636159 606638404 2245 False 669.333333 1554 84.837333 1719 4031 3 chr7D.!!$F2 2312
5 TraesCS6D01G344000 chr7A 96567617 96570516 2899 True 1163.333333 2848 86.460667 1059 4032 3 chr7A.!!$R2 2973
6 TraesCS6D01G344000 chr7A 698677123 698679382 2259 True 693.333333 1604 86.199000 1712 4031 3 chr7A.!!$R3 2319
7 TraesCS6D01G344000 chr7B 47000731 47003652 2921 True 1126.666667 2743 86.055000 1059 4032 3 chr7B.!!$R1 2973
8 TraesCS6D01G344000 chr7B 690752654 690755575 2921 True 681.250000 1591 86.588000 1168 4032 4 chr7B.!!$R2 2864
9 TraesCS6D01G344000 chr1D 349792857 349794639 1782 True 1555.000000 1555 82.609000 1168 2941 1 chr1D.!!$R1 1773
10 TraesCS6D01G344000 chr1B 471761605 471763387 1782 True 1528.000000 1528 82.320000 1168 2941 1 chr1B.!!$R1 1773
11 TraesCS6D01G344000 chr1A 450094613 450096395 1782 True 1522.000000 1522 82.245000 1168 2941 1 chr1A.!!$R1 1773
12 TraesCS6D01G344000 chr4B 586466727 586467254 527 True 405.000000 405 81.015000 2425 2940 1 chr4B.!!$R1 515

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
756 785 0.475906 CCTCCTCCCCATCCATGAAC 59.524 60.000 0.00 0.0 0.00 3.18 F
757 786 1.516110 CTCCTCCCCATCCATGAACT 58.484 55.000 0.00 0.0 0.00 3.01 F
2346 2498 2.610859 AGGGTCCACGGCCTGATT 60.611 61.111 0.00 0.0 0.00 2.57 F
2973 3137 0.106708 CCATCACCATCCGGATCGTT 59.893 55.000 15.88 0.0 35.59 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2129 1.661509 CGTCTTGTCGCTGCACAGA 60.662 57.895 0.81 1.45 0.0 3.41 R
2578 2730 2.921972 GTTGGTGCCCATGCCCAA 60.922 61.111 4.17 4.17 42.1 4.12 R
3276 3472 0.108329 TCGTTCTCCCGGATTTCAGC 60.108 55.000 0.73 0.00 0.0 4.26 R
4492 5956 0.178953 ATTGTCTGCTGGGGTTTGCT 60.179 50.000 0.00 0.00 0.0 3.91 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.432444 CCCAAAATACTTGTCGGAGCA 58.568 47.619 0.00 0.00 0.00 4.26
21 22 2.817258 CCCAAAATACTTGTCGGAGCAA 59.183 45.455 0.00 0.00 0.00 3.91
22 23 3.443681 CCCAAAATACTTGTCGGAGCAAT 59.556 43.478 0.00 0.00 0.00 3.56
23 24 4.414852 CCAAAATACTTGTCGGAGCAATG 58.585 43.478 0.00 0.00 0.00 2.82
24 25 4.414852 CAAAATACTTGTCGGAGCAATGG 58.585 43.478 0.00 0.00 0.00 3.16
25 26 3.350219 AATACTTGTCGGAGCAATGGT 57.650 42.857 0.00 0.00 0.00 3.55
26 27 2.851263 TACTTGTCGGAGCAATGGTT 57.149 45.000 0.00 0.00 0.00 3.67
27 28 2.851263 ACTTGTCGGAGCAATGGTTA 57.149 45.000 0.00 0.00 0.00 2.85
28 29 3.134574 ACTTGTCGGAGCAATGGTTAA 57.865 42.857 0.00 0.00 0.00 2.01
29 30 3.482436 ACTTGTCGGAGCAATGGTTAAA 58.518 40.909 0.00 0.00 0.00 1.52
30 31 4.079253 ACTTGTCGGAGCAATGGTTAAAT 58.921 39.130 0.00 0.00 0.00 1.40
31 32 5.250200 ACTTGTCGGAGCAATGGTTAAATA 58.750 37.500 0.00 0.00 0.00 1.40
32 33 5.885912 ACTTGTCGGAGCAATGGTTAAATAT 59.114 36.000 0.00 0.00 0.00 1.28
33 34 5.749596 TGTCGGAGCAATGGTTAAATATG 57.250 39.130 0.00 0.00 0.00 1.78
34 35 4.578516 TGTCGGAGCAATGGTTAAATATGG 59.421 41.667 0.00 0.00 0.00 2.74
35 36 4.819630 GTCGGAGCAATGGTTAAATATGGA 59.180 41.667 0.00 0.00 0.00 3.41
36 37 5.473504 GTCGGAGCAATGGTTAAATATGGAT 59.526 40.000 0.00 0.00 0.00 3.41
37 38 6.653320 GTCGGAGCAATGGTTAAATATGGATA 59.347 38.462 0.00 0.00 0.00 2.59
38 39 7.336931 GTCGGAGCAATGGTTAAATATGGATAT 59.663 37.037 0.00 0.00 0.00 1.63
39 40 8.544622 TCGGAGCAATGGTTAAATATGGATATA 58.455 33.333 0.00 0.00 0.00 0.86
40 41 9.342308 CGGAGCAATGGTTAAATATGGATATAT 57.658 33.333 0.00 0.00 0.00 0.86
78 79 6.929625 ACATCTAGATACATCCATTTCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
79 80 6.721668 ACATCTAGATACATCCATTTCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
80 81 6.576662 TCTAGATACATCCATTTCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
81 82 6.068670 TCTAGATACATCCATTTCTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
82 83 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
83 84 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
84 85 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
85 86 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
86 87 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
87 88 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
88 89 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
89 90 6.659242 ACATCCATTTCTCCGACAAGTATTTT 59.341 34.615 0.00 0.00 0.00 1.82
90 91 6.737254 TCCATTTCTCCGACAAGTATTTTC 57.263 37.500 0.00 0.00 0.00 2.29
91 92 5.350365 TCCATTTCTCCGACAAGTATTTTCG 59.650 40.000 0.00 0.00 0.00 3.46
98 99 4.227177 CGACAAGTATTTTCGGACGAAG 57.773 45.455 7.25 0.00 35.38 3.79
99 100 3.060363 CGACAAGTATTTTCGGACGAAGG 59.940 47.826 7.25 0.00 35.38 3.46
100 101 3.332034 ACAAGTATTTTCGGACGAAGGG 58.668 45.455 7.25 0.00 35.38 3.95
101 102 3.007182 ACAAGTATTTTCGGACGAAGGGA 59.993 43.478 7.25 0.00 35.38 4.20
102 103 3.521947 AGTATTTTCGGACGAAGGGAG 57.478 47.619 7.25 0.00 35.38 4.30
150 151 5.521372 GGCAAAGATCAAATAAGGACATTGC 59.479 40.000 0.00 0.00 0.00 3.56
156 157 7.910584 AGATCAAATAAGGACATTGCCTTTTT 58.089 30.769 14.72 11.42 45.85 1.94
160 161 8.522830 TCAAATAAGGACATTGCCTTTTTAGAG 58.477 33.333 14.72 9.05 45.85 2.43
164 165 3.193479 GGACATTGCCTTTTTAGAGTGGG 59.807 47.826 0.00 0.00 0.00 4.61
170 171 2.751816 GCCTTTTTAGAGTGGGTGTGGT 60.752 50.000 0.00 0.00 0.00 4.16
177 178 1.132817 AGAGTGGGTGTGGTTAGGTCT 60.133 52.381 0.00 0.00 0.00 3.85
179 180 1.053424 GTGGGTGTGGTTAGGTCTCA 58.947 55.000 0.00 0.00 0.00 3.27
201 202 2.028930 GTCGACTGAGATCCAACCAAGT 60.029 50.000 8.70 0.00 0.00 3.16
204 205 3.444034 CGACTGAGATCCAACCAAGTCTA 59.556 47.826 0.00 0.00 0.00 2.59
211 212 5.799213 AGATCCAACCAAGTCTAAGTCAAG 58.201 41.667 0.00 0.00 0.00 3.02
215 216 3.127425 ACCAAGTCTAAGTCAAGTGGC 57.873 47.619 0.00 0.00 0.00 5.01
246 247 9.965824 CATACAAGAAAGAAAAAGGAAAAGCTA 57.034 29.630 0.00 0.00 0.00 3.32
250 251 9.973246 CAAGAAAGAAAAAGGAAAAGCTAAAAC 57.027 29.630 0.00 0.00 0.00 2.43
251 252 9.719355 AAGAAAGAAAAAGGAAAAGCTAAAACA 57.281 25.926 0.00 0.00 0.00 2.83
296 297 4.221482 TGCAAGATCTCACGGATATAGCAT 59.779 41.667 0.00 0.00 34.33 3.79
301 302 3.408634 TCTCACGGATATAGCATCGACA 58.591 45.455 0.00 0.00 0.00 4.35
302 303 4.010349 TCTCACGGATATAGCATCGACAT 58.990 43.478 0.00 0.00 0.00 3.06
303 304 4.095036 TCTCACGGATATAGCATCGACATC 59.905 45.833 0.00 0.00 0.00 3.06
304 305 3.756434 TCACGGATATAGCATCGACATCA 59.244 43.478 0.00 0.00 0.00 3.07
306 307 5.105063 CACGGATATAGCATCGACATCAAT 58.895 41.667 0.00 0.00 0.00 2.57
308 309 5.807520 ACGGATATAGCATCGACATCAATTC 59.192 40.000 0.00 0.00 0.00 2.17
309 310 6.038985 CGGATATAGCATCGACATCAATTCT 58.961 40.000 0.00 0.00 0.00 2.40
310 311 6.198029 CGGATATAGCATCGACATCAATTCTC 59.802 42.308 0.00 0.00 0.00 2.87
311 312 7.038048 GGATATAGCATCGACATCAATTCTCA 58.962 38.462 0.00 0.00 0.00 3.27
312 313 7.222417 GGATATAGCATCGACATCAATTCTCAG 59.778 40.741 0.00 0.00 0.00 3.35
338 348 5.928839 TGACTGAGATTTAGCAAGACTGTTC 59.071 40.000 0.00 0.00 0.00 3.18
339 349 5.241662 ACTGAGATTTAGCAAGACTGTTCC 58.758 41.667 0.00 0.00 0.00 3.62
345 355 7.624549 AGATTTAGCAAGACTGTTCCAGATTA 58.375 34.615 0.00 0.00 35.18 1.75
360 370 3.621558 CAGATTACCCAAAGAACTCCCC 58.378 50.000 0.00 0.00 0.00 4.81
361 371 2.238898 AGATTACCCAAAGAACTCCCCG 59.761 50.000 0.00 0.00 0.00 5.73
370 380 0.693049 AGAACTCCCCGCAACATTCT 59.307 50.000 0.00 0.00 0.00 2.40
378 388 2.413634 CCCCGCAACATTCTAAAACGAC 60.414 50.000 0.00 0.00 0.00 4.34
390 400 9.275398 ACATTCTAAAACGACTTTACCATGTTA 57.725 29.630 0.00 0.00 29.92 2.41
533 545 2.488355 CAGCAAGCGCATGAAGGG 59.512 61.111 18.15 0.00 42.27 3.95
534 546 2.042259 CAGCAAGCGCATGAAGGGA 61.042 57.895 18.15 0.00 42.27 4.20
740 769 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
741 770 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
742 771 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
743 772 2.612251 CTCCCTCCCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
744 773 3.036959 TCCCTCCCTCCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
745 774 4.179599 CCCTCCCTCCCTCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
746 775 4.179599 CCTCCCTCCCTCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
747 776 3.368501 CTCCCTCCCTCCTCCCCA 61.369 72.222 0.00 0.00 0.00 4.96
748 777 2.628465 TCCCTCCCTCCTCCCCAT 60.628 66.667 0.00 0.00 0.00 4.00
749 778 2.122189 CCCTCCCTCCTCCCCATC 60.122 72.222 0.00 0.00 0.00 3.51
750 779 2.122189 CCTCCCTCCTCCCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
751 780 2.705410 CTCCCTCCTCCCCATCCA 59.295 66.667 0.00 0.00 0.00 3.41
752 781 1.241327 CTCCCTCCTCCCCATCCAT 59.759 63.158 0.00 0.00 0.00 3.41
753 782 1.073474 TCCCTCCTCCCCATCCATG 60.073 63.158 0.00 0.00 0.00 3.66
754 783 1.073474 CCCTCCTCCCCATCCATGA 60.073 63.158 0.00 0.00 0.00 3.07
755 784 0.698886 CCCTCCTCCCCATCCATGAA 60.699 60.000 0.00 0.00 0.00 2.57
756 785 0.475906 CCTCCTCCCCATCCATGAAC 59.524 60.000 0.00 0.00 0.00 3.18
757 786 1.516110 CTCCTCCCCATCCATGAACT 58.484 55.000 0.00 0.00 0.00 3.01
881 918 4.890306 GCCTCCCCTCCCCTCTCC 62.890 77.778 0.00 0.00 0.00 3.71
882 919 3.039526 CCTCCCCTCCCCTCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
883 920 2.612251 CTCCCCTCCCCTCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
884 921 3.036959 TCCCCTCCCCTCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
966 1003 3.775654 AAGAAGGAGCGGGCGAGG 61.776 66.667 0.00 0.00 0.00 4.63
2346 2498 2.610859 AGGGTCCACGGCCTGATT 60.611 61.111 0.00 0.00 0.00 2.57
2973 3137 0.106708 CCATCACCATCCGGATCGTT 59.893 55.000 15.88 0.00 35.59 3.85
3195 3359 0.818296 TGCTCTTCTTCTACCTCGCC 59.182 55.000 0.00 0.00 0.00 5.54
3248 3431 1.131504 CTCGTCTTCTTCCTCCGACTG 59.868 57.143 0.00 0.00 0.00 3.51
3275 3471 6.403309 CCGCCATGAATGATCATAAGAAGATG 60.403 42.308 9.04 5.34 44.53 2.90
3276 3472 6.403309 CGCCATGAATGATCATAAGAAGATGG 60.403 42.308 9.04 13.81 44.53 3.51
3284 3480 7.741027 TGATCATAAGAAGATGGCTGAAATC 57.259 36.000 0.00 0.00 0.00 2.17
3285 3481 6.713903 TGATCATAAGAAGATGGCTGAAATCC 59.286 38.462 0.00 0.00 0.00 3.01
3286 3482 5.059161 TCATAAGAAGATGGCTGAAATCCG 58.941 41.667 0.00 0.00 0.00 4.18
3288 3484 1.133976 AGAAGATGGCTGAAATCCGGG 60.134 52.381 0.00 0.00 0.00 5.73
3290 3486 0.471617 AGATGGCTGAAATCCGGGAG 59.528 55.000 0.00 0.00 0.00 4.30
3291 3487 0.469917 GATGGCTGAAATCCGGGAGA 59.530 55.000 0.00 0.00 0.00 3.71
3292 3488 0.918983 ATGGCTGAAATCCGGGAGAA 59.081 50.000 0.00 0.00 0.00 2.87
3669 4012 1.680735 CAACAACAAGGCAAGCCACTA 59.319 47.619 14.40 0.00 38.92 2.74
3678 4029 0.253044 GCAAGCCACTACCATCTCCA 59.747 55.000 0.00 0.00 0.00 3.86
3681 4032 2.947652 CAAGCCACTACCATCTCCATTG 59.052 50.000 0.00 0.00 0.00 2.82
3703 4076 3.518590 CTCCATTTGCAAGCTCCATTTC 58.481 45.455 0.00 0.00 0.00 2.17
3705 4078 2.027929 CCATTTGCAAGCTCCATTTCCA 60.028 45.455 0.00 0.00 0.00 3.53
3707 4080 4.258543 CATTTGCAAGCTCCATTTCCATT 58.741 39.130 0.00 0.00 0.00 3.16
3712 4085 3.490419 GCAAGCTCCATTTCCATTAGCAG 60.490 47.826 0.00 0.00 35.63 4.24
3713 4086 2.941480 AGCTCCATTTCCATTAGCAGG 58.059 47.619 0.00 0.00 35.63 4.85
3714 4087 2.511218 AGCTCCATTTCCATTAGCAGGA 59.489 45.455 0.00 0.00 35.63 3.86
3715 4088 3.053395 AGCTCCATTTCCATTAGCAGGAA 60.053 43.478 0.00 0.00 43.13 3.36
3720 4093 5.829924 TCCATTTCCATTAGCAGGAATTCTC 59.170 40.000 5.23 0.00 44.14 2.87
3721 4094 5.595542 CCATTTCCATTAGCAGGAATTCTCA 59.404 40.000 5.23 0.00 44.14 3.27
3722 4095 6.460676 CCATTTCCATTAGCAGGAATTCTCAC 60.461 42.308 5.23 0.00 44.14 3.51
3725 4098 4.471025 TCCATTAGCAGGAATTCTCACTGA 59.529 41.667 12.69 2.75 34.21 3.41
3727 4100 5.426504 CATTAGCAGGAATTCTCACTGACT 58.573 41.667 12.69 11.09 34.21 3.41
3728 4101 3.331478 AGCAGGAATTCTCACTGACTG 57.669 47.619 12.69 7.56 34.21 3.51
3729 4102 2.902486 AGCAGGAATTCTCACTGACTGA 59.098 45.455 12.69 0.00 34.21 3.41
3732 4105 4.094590 GCAGGAATTCTCACTGACTGATTG 59.905 45.833 12.69 0.00 34.21 2.67
3734 4107 5.350914 CAGGAATTCTCACTGACTGATTGAC 59.649 44.000 5.23 0.00 34.21 3.18
3735 4108 5.012458 AGGAATTCTCACTGACTGATTGACA 59.988 40.000 5.23 0.00 0.00 3.58
3737 4110 6.373774 GGAATTCTCACTGACTGATTGACAAT 59.626 38.462 5.23 0.00 0.00 2.71
3738 4111 6.738832 ATTCTCACTGACTGATTGACAATG 57.261 37.500 5.14 0.00 0.00 2.82
3837 4234 2.594303 CTGCACGGCCTCAACCAA 60.594 61.111 0.00 0.00 0.00 3.67
3860 4257 0.608130 AGCAGCAACTCCGACATGTA 59.392 50.000 0.00 0.00 0.00 2.29
4086 4494 0.969894 AGGGCAGCGATATCTACACC 59.030 55.000 0.34 0.00 0.00 4.16
4099 4507 7.380065 GCGATATCTACACCTCTAAGTTCTTTG 59.620 40.741 0.34 0.00 0.00 2.77
4164 4582 2.040412 GGTTCAGATTCTCAGGGTTGGT 59.960 50.000 0.00 0.00 0.00 3.67
4165 4583 3.498661 GGTTCAGATTCTCAGGGTTGGTT 60.499 47.826 0.00 0.00 0.00 3.67
4166 4584 4.145052 GTTCAGATTCTCAGGGTTGGTTT 58.855 43.478 0.00 0.00 0.00 3.27
4195 4613 9.847224 TTTTCTTTGACCTAGATGTTAAGAAGT 57.153 29.630 0.00 0.00 34.06 3.01
4196 4614 9.847224 TTTCTTTGACCTAGATGTTAAGAAGTT 57.153 29.630 0.00 0.00 34.06 2.66
4202 4620 5.705905 ACCTAGATGTTAAGAAGTTGTTGGC 59.294 40.000 0.00 0.00 0.00 4.52
4284 4702 4.694037 AGGAGTACGGTTTTGAGTTTATGC 59.306 41.667 0.00 0.00 0.00 3.14
4285 4703 4.142752 GGAGTACGGTTTTGAGTTTATGCC 60.143 45.833 0.00 0.00 0.00 4.40
4286 4704 4.391155 AGTACGGTTTTGAGTTTATGCCA 58.609 39.130 0.00 0.00 0.00 4.92
4287 4705 3.915437 ACGGTTTTGAGTTTATGCCAG 57.085 42.857 0.00 0.00 0.00 4.85
4288 4706 3.482436 ACGGTTTTGAGTTTATGCCAGA 58.518 40.909 0.00 0.00 0.00 3.86
4289 4707 3.252458 ACGGTTTTGAGTTTATGCCAGAC 59.748 43.478 0.00 0.00 0.00 3.51
4290 4708 3.365969 CGGTTTTGAGTTTATGCCAGACC 60.366 47.826 0.00 0.00 0.00 3.85
4291 4709 3.826729 GGTTTTGAGTTTATGCCAGACCT 59.173 43.478 0.00 0.00 0.00 3.85
4292 4710 4.280929 GGTTTTGAGTTTATGCCAGACCTT 59.719 41.667 0.00 0.00 0.00 3.50
4293 4711 5.221441 GGTTTTGAGTTTATGCCAGACCTTT 60.221 40.000 0.00 0.00 0.00 3.11
4294 4712 6.280643 GTTTTGAGTTTATGCCAGACCTTTT 58.719 36.000 0.00 0.00 0.00 2.27
4295 4713 6.478512 TTTGAGTTTATGCCAGACCTTTTT 57.521 33.333 0.00 0.00 0.00 1.94
4296 4714 5.452078 TGAGTTTATGCCAGACCTTTTTG 57.548 39.130 0.00 0.00 0.00 2.44
4348 5790 6.367695 TGTTGTGTGGAATAAATACTCACTCG 59.632 38.462 0.00 0.00 0.00 4.18
4383 5826 6.206498 GTGAAACTTGTTCAAACATACTCCC 58.794 40.000 0.00 0.00 38.95 4.30
4391 5834 1.831736 CAAACATACTCCCTCCGTCCT 59.168 52.381 0.00 0.00 0.00 3.85
4515 10300 2.890311 CAAACCCCAGCAGACAATGTAA 59.110 45.455 0.00 0.00 0.00 2.41
4516 10301 3.456380 AACCCCAGCAGACAATGTAAT 57.544 42.857 0.00 0.00 0.00 1.89
4534 10319 3.705043 AATCCAGCAATTTCATCGCTC 57.295 42.857 0.00 0.00 32.48 5.03
4549 10336 1.000394 TCGCTCGAGATGGTCAACAAA 60.000 47.619 18.75 0.00 0.00 2.83
4575 10362 4.035208 AGACAGTTTAACAGAGCAAAACCG 59.965 41.667 0.00 0.00 34.39 4.44
4578 10365 0.589223 TTAACAGAGCAAAACCGGCG 59.411 50.000 0.00 0.00 36.08 6.46
4586 10373 0.663269 GCAAAACCGGCGGAAAGAAG 60.663 55.000 35.78 17.24 0.00 2.85
4587 10374 0.948678 CAAAACCGGCGGAAAGAAGA 59.051 50.000 35.78 0.00 0.00 2.87
4592 10379 2.436115 GGCGGAAAGAAGACCCCG 60.436 66.667 0.00 0.00 44.34 5.73
4593 10380 2.660802 GCGGAAAGAAGACCCCGA 59.339 61.111 0.00 0.00 44.29 5.14
4618 10430 5.351465 TCAAGAAGGTTAGCATCGCTTAAAG 59.649 40.000 0.00 0.00 40.44 1.85
4730 10631 9.539825 GTCTGATGATTCAAAATAGAAGAGCTA 57.460 33.333 0.00 0.00 0.00 3.32
4739 10640 8.324163 TCAAAATAGAAGAGCTAAAGGTGAAC 57.676 34.615 0.00 0.00 31.66 3.18
4758 10659 4.219507 TGAACGGTGGCATTCATTTAACAT 59.780 37.500 0.00 0.00 29.89 2.71
4812 10713 5.198274 CAACTAAACAGAACGAAGAACAGC 58.802 41.667 0.00 0.00 0.00 4.40
4813 10714 3.808174 ACTAAACAGAACGAAGAACAGCC 59.192 43.478 0.00 0.00 0.00 4.85
4814 10715 2.325583 AACAGAACGAAGAACAGCCA 57.674 45.000 0.00 0.00 0.00 4.75
4827 10728 6.742718 CGAAGAACAGCCAAATTGTAATACTG 59.257 38.462 0.00 0.00 0.00 2.74
4829 10730 7.759489 AGAACAGCCAAATTGTAATACTGAA 57.241 32.000 0.00 0.00 0.00 3.02
4830 10731 8.177119 AGAACAGCCAAATTGTAATACTGAAA 57.823 30.769 0.00 0.00 0.00 2.69
4969 12147 7.930325 GGATCAGTGATGATTCAACATAGAAGA 59.070 37.037 11.20 0.00 32.48 2.87
4973 12151 7.763071 CAGTGATGATTCAACATAGAAGACTCA 59.237 37.037 0.00 0.00 32.48 3.41
4990 12168 4.082190 AGACTCATTCTAGTAGCACGCAAA 60.082 41.667 0.00 0.00 30.17 3.68
4994 12172 0.606096 TCTAGTAGCACGCAAAGGCA 59.394 50.000 0.00 0.00 41.24 4.75
4999 12177 0.950555 TAGCACGCAAAGGCAGACTG 60.951 55.000 0.00 0.00 41.24 3.51
5009 12187 1.668826 AGGCAGACTGGGTATTCCAA 58.331 50.000 4.26 0.00 46.51 3.53
5011 12189 1.282157 GGCAGACTGGGTATTCCAACT 59.718 52.381 4.26 0.00 46.51 3.16
5027 12205 6.701145 TTCCAACTTTGCACAATAACTACA 57.299 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.432444 TGCTCCGACAAGTATTTTGGG 58.568 47.619 0.00 0.00 0.00 4.12
1 2 4.414852 CATTGCTCCGACAAGTATTTTGG 58.585 43.478 0.00 0.00 31.96 3.28
2 3 4.082787 ACCATTGCTCCGACAAGTATTTTG 60.083 41.667 0.00 0.00 31.96 2.44
3 4 4.079253 ACCATTGCTCCGACAAGTATTTT 58.921 39.130 0.00 0.00 31.96 1.82
4 5 3.686016 ACCATTGCTCCGACAAGTATTT 58.314 40.909 0.00 0.00 31.96 1.40
5 6 3.350219 ACCATTGCTCCGACAAGTATT 57.650 42.857 0.00 0.00 31.96 1.89
6 7 3.350219 AACCATTGCTCCGACAAGTAT 57.650 42.857 0.00 0.00 31.96 2.12
7 8 2.851263 AACCATTGCTCCGACAAGTA 57.149 45.000 0.00 0.00 31.96 2.24
8 9 2.851263 TAACCATTGCTCCGACAAGT 57.149 45.000 0.00 0.00 31.96 3.16
9 10 4.701956 ATTTAACCATTGCTCCGACAAG 57.298 40.909 0.00 0.00 31.96 3.16
10 11 5.067153 CCATATTTAACCATTGCTCCGACAA 59.933 40.000 0.00 0.00 0.00 3.18
11 12 4.578516 CCATATTTAACCATTGCTCCGACA 59.421 41.667 0.00 0.00 0.00 4.35
12 13 4.819630 TCCATATTTAACCATTGCTCCGAC 59.180 41.667 0.00 0.00 0.00 4.79
13 14 5.042463 TCCATATTTAACCATTGCTCCGA 57.958 39.130 0.00 0.00 0.00 4.55
14 15 5.964958 ATCCATATTTAACCATTGCTCCG 57.035 39.130 0.00 0.00 0.00 4.63
52 53 8.690884 CGGAGAAATGGATGTATCTAGATGTAT 58.309 37.037 15.79 9.11 0.00 2.29
53 54 7.888546 TCGGAGAAATGGATGTATCTAGATGTA 59.111 37.037 15.79 4.44 0.00 2.29
54 55 6.721668 TCGGAGAAATGGATGTATCTAGATGT 59.278 38.462 15.79 1.25 0.00 3.06
55 56 7.032580 GTCGGAGAAATGGATGTATCTAGATG 58.967 42.308 15.79 0.00 39.69 2.90
56 57 6.721668 TGTCGGAGAAATGGATGTATCTAGAT 59.278 38.462 10.73 10.73 39.69 1.98
57 58 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
58 59 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
59 60 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
60 61 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
61 62 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
62 63 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
63 64 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
64 65 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
65 66 6.683974 AAATACTTGTCGGAGAAATGGATG 57.316 37.500 0.00 0.00 39.69 3.51
66 67 6.037172 CGAAAATACTTGTCGGAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
67 68 5.350365 CGAAAATACTTGTCGGAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
68 69 5.560148 CGAAAATACTTGTCGGAGAAATGG 58.440 41.667 0.00 0.00 39.69 3.16
77 78 3.060363 CCTTCGTCCGAAAATACTTGTCG 59.940 47.826 3.52 0.00 33.34 4.35
78 79 3.370061 CCCTTCGTCCGAAAATACTTGTC 59.630 47.826 3.52 0.00 33.34 3.18
79 80 3.007182 TCCCTTCGTCCGAAAATACTTGT 59.993 43.478 3.52 0.00 33.34 3.16
80 81 3.592059 TCCCTTCGTCCGAAAATACTTG 58.408 45.455 3.52 0.00 33.34 3.16
81 82 3.260128 ACTCCCTTCGTCCGAAAATACTT 59.740 43.478 3.52 0.00 33.34 2.24
82 83 2.830321 ACTCCCTTCGTCCGAAAATACT 59.170 45.455 3.52 0.00 33.34 2.12
83 84 3.242549 ACTCCCTTCGTCCGAAAATAC 57.757 47.619 3.52 0.00 33.34 1.89
84 85 3.382546 CCTACTCCCTTCGTCCGAAAATA 59.617 47.826 3.52 0.00 33.34 1.40
85 86 2.167900 CCTACTCCCTTCGTCCGAAAAT 59.832 50.000 3.52 0.00 33.34 1.82
86 87 1.547372 CCTACTCCCTTCGTCCGAAAA 59.453 52.381 3.52 0.00 33.34 2.29
87 88 1.180029 CCTACTCCCTTCGTCCGAAA 58.820 55.000 3.52 0.00 33.34 3.46
88 89 0.038744 ACCTACTCCCTTCGTCCGAA 59.961 55.000 1.81 1.81 0.00 4.30
89 90 0.038744 AACCTACTCCCTTCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
90 91 0.893447 AAACCTACTCCCTTCGTCCG 59.107 55.000 0.00 0.00 0.00 4.79
91 92 3.413846 AAAAACCTACTCCCTTCGTCC 57.586 47.619 0.00 0.00 0.00 4.79
119 120 6.151648 TCCTTATTTGATCTTTGCCAGAACTG 59.848 38.462 0.00 0.00 34.16 3.16
125 126 6.632909 CAATGTCCTTATTTGATCTTTGCCA 58.367 36.000 0.00 0.00 0.00 4.92
127 128 5.521372 GGCAATGTCCTTATTTGATCTTTGC 59.479 40.000 0.00 0.00 36.19 3.68
150 151 3.223674 ACCACACCCACTCTAAAAAGG 57.776 47.619 0.00 0.00 0.00 3.11
156 157 2.111255 AGACCTAACCACACCCACTCTA 59.889 50.000 0.00 0.00 0.00 2.43
160 161 1.002087 CTGAGACCTAACCACACCCAC 59.998 57.143 0.00 0.00 0.00 4.61
164 165 1.884579 TCGACTGAGACCTAACCACAC 59.115 52.381 0.00 0.00 0.00 3.82
179 180 1.924731 TGGTTGGATCTCAGTCGACT 58.075 50.000 13.58 13.58 0.00 4.18
201 202 6.941857 TGTATGTTATGCCACTTGACTTAGA 58.058 36.000 0.00 0.00 0.00 2.10
204 205 6.237901 TCTTGTATGTTATGCCACTTGACTT 58.762 36.000 0.00 0.00 0.00 3.01
211 212 8.810652 TTTTTCTTTCTTGTATGTTATGCCAC 57.189 30.769 0.00 0.00 0.00 5.01
246 247 6.676237 AGATCCGTGCAAAATTTTTGTTTT 57.324 29.167 19.98 3.62 0.00 2.43
250 251 6.737750 GCATTAAGATCCGTGCAAAATTTTTG 59.262 34.615 15.92 15.92 37.52 2.44
251 252 6.426328 TGCATTAAGATCCGTGCAAAATTTTT 59.574 30.769 0.00 0.00 43.83 1.94
277 278 4.334203 GTCGATGCTATATCCGTGAGATCT 59.666 45.833 0.00 0.00 36.33 2.75
296 297 4.925646 CAGTCAACTGAGAATTGATGTCGA 59.074 41.667 4.05 0.00 46.59 4.20
310 311 5.931146 AGTCTTGCTAAATCTCAGTCAACTG 59.069 40.000 3.69 3.69 45.08 3.16
311 312 5.931146 CAGTCTTGCTAAATCTCAGTCAACT 59.069 40.000 0.00 0.00 0.00 3.16
312 313 5.698545 ACAGTCTTGCTAAATCTCAGTCAAC 59.301 40.000 0.00 0.00 0.00 3.18
338 348 3.621558 GGGAGTTCTTTGGGTAATCTGG 58.378 50.000 0.00 0.00 0.00 3.86
339 349 3.621558 GGGGAGTTCTTTGGGTAATCTG 58.378 50.000 0.00 0.00 0.00 2.90
345 355 2.002018 TTGCGGGGAGTTCTTTGGGT 62.002 55.000 0.00 0.00 0.00 4.51
360 370 5.562623 GGTAAAGTCGTTTTAGAATGTTGCG 59.437 40.000 0.00 0.00 32.07 4.85
361 371 6.432107 TGGTAAAGTCGTTTTAGAATGTTGC 58.568 36.000 0.00 0.00 32.07 4.17
399 409 6.395426 TTCACATGCACATCTTTTCTCTTT 57.605 33.333 0.00 0.00 0.00 2.52
414 424 0.322456 TAGCCCACACCTTCACATGC 60.322 55.000 0.00 0.00 0.00 4.06
529 541 1.162085 ACCCCTGCTCTTCTCCCTT 59.838 57.895 0.00 0.00 0.00 3.95
533 545 1.220477 GCTCACCCCTGCTCTTCTC 59.780 63.158 0.00 0.00 0.00 2.87
534 546 2.297129 GGCTCACCCCTGCTCTTCT 61.297 63.158 0.00 0.00 0.00 2.85
736 765 0.698886 TTCATGGATGGGGAGGAGGG 60.699 60.000 0.00 0.00 0.00 4.30
737 766 0.475906 GTTCATGGATGGGGAGGAGG 59.524 60.000 0.00 0.00 0.00 4.30
738 767 1.419387 GAGTTCATGGATGGGGAGGAG 59.581 57.143 0.00 0.00 0.00 3.69
739 768 1.511613 GAGTTCATGGATGGGGAGGA 58.488 55.000 0.00 0.00 0.00 3.71
740 769 0.475906 GGAGTTCATGGATGGGGAGG 59.524 60.000 0.00 0.00 0.00 4.30
741 770 1.516110 AGGAGTTCATGGATGGGGAG 58.484 55.000 0.00 0.00 0.00 4.30
742 771 2.777692 GTTAGGAGTTCATGGATGGGGA 59.222 50.000 0.00 0.00 0.00 4.81
743 772 2.158608 GGTTAGGAGTTCATGGATGGGG 60.159 54.545 0.00 0.00 0.00 4.96
744 773 2.158608 GGGTTAGGAGTTCATGGATGGG 60.159 54.545 0.00 0.00 0.00 4.00
745 774 2.158608 GGGGTTAGGAGTTCATGGATGG 60.159 54.545 0.00 0.00 0.00 3.51
746 775 2.158608 GGGGGTTAGGAGTTCATGGATG 60.159 54.545 0.00 0.00 0.00 3.51
747 776 2.136026 GGGGGTTAGGAGTTCATGGAT 58.864 52.381 0.00 0.00 0.00 3.41
748 777 1.591768 GGGGGTTAGGAGTTCATGGA 58.408 55.000 0.00 0.00 0.00 3.41
834 868 3.170672 TGCTGGTGCTGGTGGTCT 61.171 61.111 0.00 0.00 40.48 3.85
875 912 3.039526 AGGGGAGGGGAGGAGAGG 61.040 72.222 0.00 0.00 0.00 3.69
876 913 2.612251 GAGGGGAGGGGAGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
877 914 3.036959 GGAGGGGAGGGGAGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
878 915 4.179599 GGGAGGGGAGGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
1980 2129 1.661509 CGTCTTGTCGCTGCACAGA 60.662 57.895 0.81 1.45 0.00 3.41
2346 2498 3.740397 CGGTCGGCGTACTGGTCA 61.740 66.667 6.85 0.00 0.00 4.02
2578 2730 2.921972 GTTGGTGCCCATGCCCAA 60.922 61.111 4.17 4.17 42.10 4.12
2973 3137 1.296392 CACCAGCATGAACCCGAGA 59.704 57.895 0.00 0.00 39.69 4.04
3195 3359 0.666577 GGAAGAACTCGGTGTCGTGG 60.667 60.000 0.00 0.00 37.69 4.94
3248 3431 4.318332 TCTTATGATCATTCATGGCGGAC 58.682 43.478 14.65 0.00 42.60 4.79
3275 3471 1.090052 CGTTCTCCCGGATTTCAGCC 61.090 60.000 0.73 0.00 0.00 4.85
3276 3472 0.108329 TCGTTCTCCCGGATTTCAGC 60.108 55.000 0.73 0.00 0.00 4.26
3284 3480 1.595382 GCATCCATCGTTCTCCCGG 60.595 63.158 0.00 0.00 0.00 5.73
3285 3481 0.877649 CTGCATCCATCGTTCTCCCG 60.878 60.000 0.00 0.00 0.00 5.14
3286 3482 0.533755 CCTGCATCCATCGTTCTCCC 60.534 60.000 0.00 0.00 0.00 4.30
3288 3484 1.410517 TCTCCTGCATCCATCGTTCTC 59.589 52.381 0.00 0.00 0.00 2.87
3290 3486 1.576356 GTCTCCTGCATCCATCGTTC 58.424 55.000 0.00 0.00 0.00 3.95
3291 3487 0.179100 CGTCTCCTGCATCCATCGTT 60.179 55.000 0.00 0.00 0.00 3.85
3292 3488 1.323271 ACGTCTCCTGCATCCATCGT 61.323 55.000 0.00 0.00 0.00 3.73
3669 4012 3.028850 CAAATGGAGCAATGGAGATGGT 58.971 45.455 0.00 0.00 0.00 3.55
3681 4032 0.822164 ATGGAGCTTGCAAATGGAGC 59.178 50.000 0.00 0.00 36.68 4.70
3703 4076 4.574013 GTCAGTGAGAATTCCTGCTAATGG 59.426 45.833 0.65 0.00 0.00 3.16
3705 4078 5.188555 TCAGTCAGTGAGAATTCCTGCTAAT 59.811 40.000 0.65 0.00 0.00 1.73
3707 4080 4.089361 TCAGTCAGTGAGAATTCCTGCTA 58.911 43.478 0.65 0.00 0.00 3.49
3712 4085 5.240891 TGTCAATCAGTCAGTGAGAATTCC 58.759 41.667 0.65 0.00 39.07 3.01
3713 4086 6.791887 TTGTCAATCAGTCAGTGAGAATTC 57.208 37.500 0.00 0.00 39.07 2.17
3714 4087 6.150641 CCATTGTCAATCAGTCAGTGAGAATT 59.849 38.462 0.00 0.00 39.37 2.17
3715 4088 5.646793 CCATTGTCAATCAGTCAGTGAGAAT 59.353 40.000 0.00 0.00 42.17 2.40
3720 4093 3.817084 ACACCATTGTCAATCAGTCAGTG 59.183 43.478 0.00 0.57 0.00 3.66
3721 4094 4.090761 ACACCATTGTCAATCAGTCAGT 57.909 40.909 0.00 0.00 0.00 3.41
3734 4107 3.027170 GCCGTCTGCGACACCATTG 62.027 63.158 8.91 0.00 41.33 2.82
3735 4108 2.742372 GCCGTCTGCGACACCATT 60.742 61.111 8.91 0.00 41.33 3.16
3738 4111 4.681978 AAGGCCGTCTGCGACACC 62.682 66.667 0.00 8.77 42.61 4.16
3837 4234 3.630013 TCGGAGTTGCTGCTGCCT 61.630 61.111 13.47 3.50 38.71 4.75
4086 4494 2.130272 GGGGGCCAAAGAACTTAGAG 57.870 55.000 4.39 0.00 0.00 2.43
4195 4613 9.606631 ACTGAAAAATACAAATAAAGCCAACAA 57.393 25.926 0.00 0.00 0.00 2.83
4196 4614 9.039870 CACTGAAAAATACAAATAAAGCCAACA 57.960 29.630 0.00 0.00 0.00 3.33
4202 4620 8.034804 CCTCCCCACTGAAAAATACAAATAAAG 58.965 37.037 0.00 0.00 0.00 1.85
4289 4707 6.976636 TTACAAGCAAAAGAACCAAAAAGG 57.023 33.333 0.00 0.00 45.67 3.11
4291 4709 9.606631 ACATATTACAAGCAAAAGAACCAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
4292 4710 9.606631 AACATATTACAAGCAAAAGAACCAAAA 57.393 25.926 0.00 0.00 0.00 2.44
4294 4712 9.906660 CTAACATATTACAAGCAAAAGAACCAA 57.093 29.630 0.00 0.00 0.00 3.67
4295 4713 8.026607 GCTAACATATTACAAGCAAAAGAACCA 58.973 33.333 0.00 0.00 33.38 3.67
4296 4714 7.218204 CGCTAACATATTACAAGCAAAAGAACC 59.782 37.037 0.00 0.00 32.69 3.62
4348 5790 6.848451 TGAACAAGTTTCACTTTCCTTGTAC 58.152 36.000 4.51 0.00 44.88 2.90
4383 5826 6.680874 ACGCTCTTATATTATAGGACGGAG 57.319 41.667 15.28 0.00 0.00 4.63
4455 5919 9.548631 CTCCCTCCGTCCCATAATATAATATAT 57.451 37.037 0.00 0.00 0.00 0.86
4456 5920 8.517047 ACTCCCTCCGTCCCATAATATAATATA 58.483 37.037 0.00 0.00 0.00 0.86
4457 5921 7.371043 ACTCCCTCCGTCCCATAATATAATAT 58.629 38.462 0.00 0.00 0.00 1.28
4458 5922 6.748969 ACTCCCTCCGTCCCATAATATAATA 58.251 40.000 0.00 0.00 0.00 0.98
4459 5923 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
4492 5956 0.178953 ATTGTCTGCTGGGGTTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
4534 10319 4.058124 TGTCTCTTTTGTTGACCATCTCG 58.942 43.478 0.00 0.00 0.00 4.04
4549 10336 6.183360 GGTTTTGCTCTGTTAAACTGTCTCTT 60.183 38.462 0.00 0.00 33.44 2.85
4575 10362 2.253403 ATCGGGGTCTTCTTTCCGCC 62.253 60.000 0.00 0.00 41.98 6.13
4578 10365 2.236395 TCTTGATCGGGGTCTTCTTTCC 59.764 50.000 0.00 0.00 0.00 3.13
4586 10373 2.742204 GCTAACCTTCTTGATCGGGGTC 60.742 54.545 0.00 0.00 0.00 4.46
4587 10374 1.209747 GCTAACCTTCTTGATCGGGGT 59.790 52.381 0.00 0.00 0.00 4.95
4592 10379 3.462021 AGCGATGCTAACCTTCTTGATC 58.538 45.455 0.00 0.00 36.99 2.92
4593 10380 3.550437 AGCGATGCTAACCTTCTTGAT 57.450 42.857 0.00 0.00 36.99 2.57
4730 10631 0.958822 GAATGCCACCGTTCACCTTT 59.041 50.000 0.00 0.00 37.03 3.11
4739 10640 4.742417 TGAATGTTAAATGAATGCCACCG 58.258 39.130 0.00 0.00 0.00 4.94
4758 10659 9.625747 TTATGGCTGTCTGTTGATAATTATGAA 57.374 29.630 1.78 0.00 0.00 2.57
4812 10713 8.450964 ACGATCACTTTCAGTATTACAATTTGG 58.549 33.333 0.78 0.00 0.00 3.28
4813 10714 9.478019 GACGATCACTTTCAGTATTACAATTTG 57.522 33.333 0.00 0.00 0.00 2.32
4814 10715 9.214957 TGACGATCACTTTCAGTATTACAATTT 57.785 29.630 0.00 0.00 0.00 1.82
4827 10728 5.050091 ACTGTGTTGAATGACGATCACTTTC 60.050 40.000 0.00 1.64 0.00 2.62
4829 10730 4.380531 ACTGTGTTGAATGACGATCACTT 58.619 39.130 0.00 0.00 0.00 3.16
4830 10731 3.995199 ACTGTGTTGAATGACGATCACT 58.005 40.909 0.00 0.00 0.00 3.41
4833 12011 7.435192 TCATATGTACTGTGTTGAATGACGATC 59.565 37.037 1.90 0.00 0.00 3.69
4969 12147 3.868757 TTGCGTGCTACTAGAATGAGT 57.131 42.857 0.00 0.00 0.00 3.41
4973 12151 2.280628 GCCTTTGCGTGCTACTAGAAT 58.719 47.619 0.00 0.00 0.00 2.40
4990 12168 3.417330 TGGAATACCCAGTCTGCCT 57.583 52.632 0.00 0.00 40.82 4.75
4999 12177 4.535526 ATTGTGCAAAGTTGGAATACCC 57.464 40.909 0.00 0.00 34.81 3.69


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

AutoCloner maintained by Alex Coulton.