Multiple sequence alignment - TraesCS7A01G206300

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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 TraesCS7A01G206300 chr7A 100.000 7431 0 0 1 7431 168868611 168876041 0.000000e+00 13723.0
1 TraesCS7A01G206300 chr7A 86.747 83 9 2 3430 3510 113801812 113801730 2.860000e-14 91.6
2 TraesCS7A01G206300 chr7A 84.884 86 6 6 3430 3510 672592606 672592689 6.180000e-11 80.5
3 TraesCS7A01G206300 chr7A 88.235 68 6 2 3430 3495 674109759 674109826 6.180000e-11 80.5
4 TraesCS7A01G206300 chr7D 95.866 3483 66 22 2726 6197 167358625 167362040 0.000000e+00 5563.0
5 TraesCS7A01G206300 chr7D 93.843 2420 107 23 323 2715 167356122 167358526 0.000000e+00 3605.0
6 TraesCS7A01G206300 chr7D 95.955 618 23 2 6193 6808 167362070 167362687 0.000000e+00 1002.0
7 TraesCS7A01G206300 chr7D 85.093 322 41 4 1 321 167355770 167356085 9.300000e-84 322.0
8 TraesCS7A01G206300 chr7D 93.939 165 8 2 6811 6974 167362739 167362902 1.600000e-61 248.0
9 TraesCS7A01G206300 chr7D 87.654 162 4 2 7230 7391 167363184 167363329 2.760000e-39 174.0
10 TraesCS7A01G206300 chr7D 97.222 36 0 1 5773 5807 104549457 104549492 8.050000e-05 60.2
11 TraesCS7A01G206300 chr7D 92.857 42 2 1 5768 5809 167361624 167361584 8.050000e-05 60.2
12 TraesCS7A01G206300 chr7B 89.749 3190 185 51 323 3437 131738530 131741652 0.000000e+00 3949.0
13 TraesCS7A01G206300 chr7B 94.000 1300 60 10 3722 5006 131741816 131743112 0.000000e+00 1953.0
14 TraesCS7A01G206300 chr7B 91.121 946 48 9 5262 6197 131744139 131745058 0.000000e+00 1249.0
15 TraesCS7A01G206300 chr7B 90.889 461 27 7 6208 6654 131745193 131745652 8.250000e-169 604.0
16 TraesCS7A01G206300 chr7B 89.912 228 15 3 5040 5267 131743109 131743328 3.390000e-73 287.0
17 TraesCS7A01G206300 chr7B 91.176 170 6 3 5101 5267 131743800 131743963 9.700000e-54 222.0
18 TraesCS7A01G206300 chr7B 85.427 199 18 7 7182 7380 131747611 131747798 5.880000e-46 196.0
19 TraesCS7A01G206300 chr7B 82.883 222 23 10 2025 2245 131740541 131740748 1.270000e-42 185.0
20 TraesCS7A01G206300 chr7B 92.174 115 6 2 5252 5365 131744025 131744137 7.720000e-35 159.0
21 TraesCS7A01G206300 chr3D 98.824 85 1 0 3639 3723 66406772 66406688 1.290000e-32 152.0
22 TraesCS7A01G206300 chr6B 97.674 86 2 0 3638 3723 71040855 71040770 1.670000e-31 148.0
23 TraesCS7A01G206300 chr6B 91.954 87 7 0 3637 3723 433707426 433707512 1.010000e-23 122.0
24 TraesCS7A01G206300 chr6B 100.000 40 0 0 5768 5807 599053048 599053087 2.880000e-09 75.0
25 TraesCS7A01G206300 chr3B 96.667 90 2 1 3639 3727 738379694 738379783 1.670000e-31 148.0
26 TraesCS7A01G206300 chr5A 95.455 88 3 1 3637 3723 688702452 688702539 1.010000e-28 139.0
27 TraesCS7A01G206300 chr5D 94.186 86 3 2 3638 3723 548633984 548634067 6.050000e-26 130.0
28 TraesCS7A01G206300 chr2A 92.473 93 3 4 3635 3726 115749924 115749835 6.050000e-26 130.0
29 TraesCS7A01G206300 chr6D 95.062 81 4 0 3643 3723 352881696 352881776 2.180000e-25 128.0
30 TraesCS7A01G206300 chr2B 87.952 83 8 2 3430 3510 200902871 200902953 6.140000e-16 97.1
31 TraesCS7A01G206300 chr4A 86.747 83 9 2 3430 3510 17251691 17251609 2.860000e-14 91.6
32 TraesCS7A01G206300 chr4A 85.938 64 8 1 6801 6863 582510977 582510914 4.810000e-07 67.6
33 TraesCS7A01G206300 chr3A 86.747 83 9 2 3430 3510 697535759 697535677 2.860000e-14 91.6
34 TraesCS7A01G206300 chr1A 86.747 83 9 2 3430 3510 417383026 417382944 2.860000e-14 91.6
35 TraesCS7A01G206300 chr5B 92.000 50 4 0 3430 3479 617191347 617191396 3.720000e-08 71.3
36 TraesCS7A01G206300 chr1B 95.556 45 1 1 5768 5811 674035913 674035869 3.720000e-08 71.3
37 TraesCS7A01G206300 chr1B 100.000 30 0 0 5775 5804 525798288 525798259 1.000000e-03 56.5
38 TraesCS7A01G206300 chr4B 85.938 64 8 1 6801 6863 30836766 30836829 4.810000e-07 67.6


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 TraesCS7A01G206300 chr7A 168868611 168876041 7430 False 13723.000000 13723 100.000000 1 7431 1 chr7A.!!$F1 7430
1 TraesCS7A01G206300 chr7D 167355770 167363329 7559 False 1819.000000 5563 92.058333 1 7391 6 chr7D.!!$F2 7390
2 TraesCS7A01G206300 chr7B 131738530 131747798 9268 False 978.222222 3949 89.703444 323 7380 9 chr7B.!!$F1 7057

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
599 656 0.110486 AATCCACACCAAACCGCTCT 59.890 50.000 0.00 0.0 0.00 4.09 F
990 1080 0.404426 TCGAGTGAGAGGGTGGAAGA 59.596 55.000 0.00 0.0 0.00 2.87 F
1747 1855 0.472471 TTTTGCCAGACCCTCGAGTT 59.528 50.000 12.31 0.0 0.00 3.01 F
3399 3619 0.035152 TGCATCGTGAGCCCATTTCT 60.035 50.000 0.00 0.0 0.00 2.52 F
4469 4717 0.037326 CTGGCGGCAGTCTAGAACAA 60.037 55.000 29.42 0.0 0.00 2.83 F
5344 6306 1.598130 GTGGTGTCTCCTGGTGTGC 60.598 63.158 0.00 0.0 37.07 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1591 0.394488 TCACCCACCTGCGAAACAAA 60.394 50.000 0.00 0.00 0.00 2.83 R
2539 2649 2.024414 ACACTTCTGGCACCAACTTTC 58.976 47.619 0.00 0.00 0.00 2.62 R
3590 3810 2.632377 CGACCATATGACAAGGCAAGT 58.368 47.619 3.65 0.00 0.00 3.16 R
5135 5384 0.322975 GGAGCCTCTCTTGCTGTGAA 59.677 55.000 0.00 0.00 39.69 3.18 R
5542 6595 2.278336 CGCAATGCATCAAGGGCG 60.278 61.111 5.91 7.43 38.45 6.13 R
6941 8205 1.066143 CACATTCGTGGAGGCCTAAGT 60.066 52.381 4.42 0.00 39.64 2.24 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
30 31 1.536284 GCGAGGAGGAGGTTTATGACG 60.536 57.143 0.00 0.00 0.00 4.35
54 55 2.437897 CCTCCAGTGCAAAGCCCT 59.562 61.111 0.00 0.00 0.00 5.19
56 57 2.032528 TCCAGTGCAAAGCCCTCG 59.967 61.111 0.00 0.00 0.00 4.63
58 59 3.741476 CAGTGCAAAGCCCTCGCC 61.741 66.667 0.00 0.00 34.57 5.54
94 95 3.479269 CGAGGCGGCTCGTTTGTC 61.479 66.667 42.65 16.62 41.43 3.18
96 97 3.909258 GAGGCGGCTCGTTTGTCGA 62.909 63.158 24.18 0.00 46.83 4.20
130 131 2.036256 GCTGGAGCACCACCCATT 59.964 61.111 0.00 0.00 41.77 3.16
140 141 2.043652 CACCCATTGGCCAGGAGG 60.044 66.667 16.13 14.89 38.23 4.30
158 159 1.301401 GAGGCTACAACGCACCACA 60.301 57.895 0.00 0.00 0.00 4.17
167 168 0.530650 AACGCACCACACACTCTGAG 60.531 55.000 2.45 2.45 0.00 3.35
215 216 2.755876 TGCTCGCCGAGATCTGGT 60.756 61.111 20.05 0.00 0.00 4.00
216 217 2.290122 CTGCTCGCCGAGATCTGGTT 62.290 60.000 20.05 0.00 0.00 3.67
231 232 1.905215 CTGGTTGGGAGAGTGATGAGT 59.095 52.381 0.00 0.00 0.00 3.41
233 234 1.902508 GGTTGGGAGAGTGATGAGTGA 59.097 52.381 0.00 0.00 0.00 3.41
234 235 2.303022 GGTTGGGAGAGTGATGAGTGAA 59.697 50.000 0.00 0.00 0.00 3.18
237 238 2.225369 TGGGAGAGTGATGAGTGAAGGA 60.225 50.000 0.00 0.00 0.00 3.36
239 240 3.360867 GGAGAGTGATGAGTGAAGGAGA 58.639 50.000 0.00 0.00 0.00 3.71
240 241 3.381272 GGAGAGTGATGAGTGAAGGAGAG 59.619 52.174 0.00 0.00 0.00 3.20
241 242 4.269183 GAGAGTGATGAGTGAAGGAGAGA 58.731 47.826 0.00 0.00 0.00 3.10
242 243 4.272489 AGAGTGATGAGTGAAGGAGAGAG 58.728 47.826 0.00 0.00 0.00 3.20
243 244 4.018506 AGAGTGATGAGTGAAGGAGAGAGA 60.019 45.833 0.00 0.00 0.00 3.10
245 246 3.381272 GTGATGAGTGAAGGAGAGAGAGG 59.619 52.174 0.00 0.00 0.00 3.69
246 247 3.268072 TGATGAGTGAAGGAGAGAGAGGA 59.732 47.826 0.00 0.00 0.00 3.71
257 258 0.671251 GAGAGAGGATAGGGCGTGTG 59.329 60.000 0.00 0.00 0.00 3.82
286 287 3.541632 GAAAATGGGTCAGCCGAGATAA 58.458 45.455 0.00 0.00 34.97 1.75
290 291 1.120530 GGGTCAGCCGAGATAAAGGA 58.879 55.000 0.00 0.00 34.97 3.36
301 302 2.292845 GAGATAAAGGATGCCAAGCTGC 59.707 50.000 0.00 0.00 0.00 5.25
303 304 0.684153 TAAAGGATGCCAAGCTGCCC 60.684 55.000 0.00 0.00 0.00 5.36
321 322 4.988598 CCTGTTCGCGTGGGTGCT 62.989 66.667 5.77 0.00 0.00 4.40
325 361 2.735478 TTCGCGTGGGTGCTAACG 60.735 61.111 5.77 0.00 42.61 3.18
351 387 0.248094 GCTTTAAGATTCGTGCGCCC 60.248 55.000 4.18 0.00 0.00 6.13
375 411 2.359354 ATGGCAGTTGGCGCGTTA 60.359 55.556 8.43 0.00 46.16 3.18
406 442 6.877611 ATCCTTAAACATCTGACGTTTGTT 57.122 33.333 11.69 0.61 37.18 2.83
462 502 3.820557 TCTTTCTTGTTCTCCAACCCAG 58.179 45.455 0.00 0.00 0.00 4.45
503 543 4.530857 CCACATCCGCCCGTCTCC 62.531 72.222 0.00 0.00 0.00 3.71
525 566 2.436173 CCCCCTGTGAAGGAAGTATCTC 59.564 54.545 0.00 0.00 0.00 2.75
599 656 0.110486 AATCCACACCAAACCGCTCT 59.890 50.000 0.00 0.00 0.00 4.09
614 671 1.081442 CTCTGTGTACACGCGAGCA 60.081 57.895 23.61 2.48 0.00 4.26
732 821 4.722700 CTCCCACTGGCAACCGGG 62.723 72.222 6.32 8.84 40.13 5.73
990 1080 0.404426 TCGAGTGAGAGGGTGGAAGA 59.596 55.000 0.00 0.00 0.00 2.87
995 1085 1.552792 GTGAGAGGGTGGAAGAGAAGG 59.447 57.143 0.00 0.00 0.00 3.46
1162 1253 3.202706 GCTTGATTCGGGGCGTCC 61.203 66.667 0.00 0.00 0.00 4.79
1163 1254 2.584608 CTTGATTCGGGGCGTCCT 59.415 61.111 5.77 0.00 0.00 3.85
1164 1255 1.815421 CTTGATTCGGGGCGTCCTG 60.815 63.158 9.17 9.17 40.84 3.86
1402 1494 2.493414 ACTGCTCGGTAGTAGTCACT 57.507 50.000 0.00 0.00 44.38 3.41
1437 1530 4.993705 TTTGGGGAAGTCTGTTATCTGT 57.006 40.909 0.00 0.00 0.00 3.41
1442 1535 5.046591 TGGGGAAGTCTGTTATCTGTTGTAG 60.047 44.000 0.00 0.00 0.00 2.74
1444 1537 4.870991 GGAAGTCTGTTATCTGTTGTAGCC 59.129 45.833 0.00 0.00 0.00 3.93
1446 1539 5.483685 AGTCTGTTATCTGTTGTAGCCAA 57.516 39.130 0.00 0.00 0.00 4.52
1462 1555 3.702147 CAAATTGTTTGGGCCTGCA 57.298 47.368 4.53 0.00 37.01 4.41
1476 1569 1.730064 GCCTGCAAATGCTTGATGTTG 59.270 47.619 6.97 0.00 42.66 3.33
1498 1591 6.835819 TGTGCTTCACTAGTACTAATCTGT 57.164 37.500 3.76 0.00 39.88 3.41
1702 1807 2.350484 GCTTCTTGTCCCGTTAGTTTGC 60.350 50.000 0.00 0.00 0.00 3.68
1747 1855 0.472471 TTTTGCCAGACCCTCGAGTT 59.528 50.000 12.31 0.00 0.00 3.01
1808 1916 4.938226 GGAACTAAGCTTGACAATGTAGCT 59.062 41.667 9.86 4.92 46.63 3.32
1841 1949 9.717942 AGTCAAGATCTAATGAATACTTATGGC 57.282 33.333 0.00 0.00 0.00 4.40
1842 1950 9.494271 GTCAAGATCTAATGAATACTTATGGCA 57.506 33.333 0.00 0.00 0.00 4.92
1909 2017 7.827236 TGAAATTTGACGGACCTTATTAGACAT 59.173 33.333 0.00 0.00 0.00 3.06
1916 2024 6.708285 ACGGACCTTATTAGACATCAAGTTT 58.292 36.000 0.00 0.00 0.00 2.66
1918 2026 7.664318 ACGGACCTTATTAGACATCAAGTTTTT 59.336 33.333 0.00 0.00 0.00 1.94
2134 2242 4.873827 TGATGTGTTTCGAGTTTATAGCCC 59.126 41.667 0.00 0.00 0.00 5.19
2296 2404 6.057627 AGCGCTTCTCAATCAAATCATTAG 57.942 37.500 2.64 0.00 0.00 1.73
2347 2455 4.385358 TGATGCTCTGTTACGCATTCTA 57.615 40.909 0.00 0.00 46.06 2.10
2356 2464 3.129638 TGTTACGCATTCTAAATTGCCCC 59.870 43.478 0.00 0.00 35.41 5.80
2370 2478 5.731957 AATTGCCCCTACGTGTTTAATTT 57.268 34.783 0.00 0.00 0.00 1.82
2372 2480 3.752665 TGCCCCTACGTGTTTAATTTGA 58.247 40.909 0.00 0.00 0.00 2.69
2458 2568 7.558161 TGATCTTAGCGATTTCATTCATGTT 57.442 32.000 0.00 0.00 30.84 2.71
2460 2570 6.741992 TCTTAGCGATTTCATTCATGTTGT 57.258 33.333 0.00 0.00 0.00 3.32
2499 2609 3.244665 TGTCAGCAATGTCTCCATTCTGT 60.245 43.478 0.00 0.00 39.28 3.41
2536 2646 8.948853 TCTTTTGTTATGCACTTCTTAAATCG 57.051 30.769 0.00 0.00 0.00 3.34
2539 2649 8.500837 TTTGTTATGCACTTCTTAAATCGTTG 57.499 30.769 0.00 0.00 0.00 4.10
2560 2670 1.392589 AAGTTGGTGCCAGAAGTGTG 58.607 50.000 0.00 0.00 0.00 3.82
2721 2833 6.730960 TGGGTTCATACGTTTTTATCAGAC 57.269 37.500 0.00 0.00 0.00 3.51
2724 2836 6.183360 GGGTTCATACGTTTTTATCAGACCTG 60.183 42.308 0.00 0.00 0.00 4.00
2744 2944 9.914834 AGACCTGCCTATTATTGTATTTTAACA 57.085 29.630 0.00 0.00 0.00 2.41
2898 3110 5.195185 ACAATGTTCTGCCATGTCATATCA 58.805 37.500 0.00 0.00 0.00 2.15
2903 3115 5.121811 GTTCTGCCATGTCATATCACTCTT 58.878 41.667 0.00 0.00 0.00 2.85
3399 3619 0.035152 TGCATCGTGAGCCCATTTCT 60.035 50.000 0.00 0.00 0.00 2.52
3413 3633 5.249163 AGCCCATTTCTGAGCCTTAATTTTT 59.751 36.000 0.00 0.00 0.00 1.94
3444 3664 1.876546 AAGCTACTCCCTCCGTCCCT 61.877 60.000 0.00 0.00 0.00 4.20
3449 3669 1.497161 ACTCCCTCCGTCCCTTAATG 58.503 55.000 0.00 0.00 0.00 1.90
3478 3698 9.944376 AGACGTTATTACATCCAATATGCTAAT 57.056 29.630 0.00 0.00 0.00 1.73
3599 3823 5.183904 AGCTACAAATTCCTTACTTGCCTTG 59.816 40.000 0.00 0.00 0.00 3.61
3668 3894 3.322369 TGTACCACAATACTTGTCGCTG 58.678 45.455 0.00 0.00 43.23 5.18
3827 4053 4.889409 TGAGCCATGTTCTGAACTTTTCTT 59.111 37.500 20.18 3.48 0.00 2.52
3852 4078 5.413309 TTTTTCTTTTTGAACTGGAGCCA 57.587 34.783 0.00 0.00 33.88 4.75
3857 4083 4.834496 TCTTTTTGAACTGGAGCCATGAAT 59.166 37.500 0.00 0.00 0.00 2.57
3946 4172 4.869861 GGTTGAATTATTGTGGCATTGACC 59.130 41.667 0.00 0.00 0.00 4.02
4051 4277 6.223852 TCTTTGGTACTTCTCTGCAAGTTAG 58.776 40.000 0.00 0.00 37.75 2.34
4095 4321 8.964476 AATCTTACTTATGATGTAACACTGGG 57.036 34.615 0.00 0.00 0.00 4.45
4096 4322 7.490657 TCTTACTTATGATGTAACACTGGGT 57.509 36.000 0.00 0.00 0.00 4.51
4097 4323 8.598202 TCTTACTTATGATGTAACACTGGGTA 57.402 34.615 0.00 0.00 0.00 3.69
4098 4324 9.209048 TCTTACTTATGATGTAACACTGGGTAT 57.791 33.333 0.00 0.00 0.00 2.73
4201 4438 8.578308 TCTTTGCTTTATTTTCTGAATGTGTG 57.422 30.769 0.00 0.00 0.00 3.82
4361 4598 6.179906 TCTTCCTCATTCTCTTTCACTGTT 57.820 37.500 0.00 0.00 0.00 3.16
4363 4600 6.484643 TCTTCCTCATTCTCTTTCACTGTTTG 59.515 38.462 0.00 0.00 0.00 2.93
4364 4601 5.928976 TCCTCATTCTCTTTCACTGTTTGA 58.071 37.500 0.00 0.00 0.00 2.69
4365 4602 5.760253 TCCTCATTCTCTTTCACTGTTTGAC 59.240 40.000 0.00 0.00 32.26 3.18
4366 4603 5.762218 CCTCATTCTCTTTCACTGTTTGACT 59.238 40.000 0.00 0.00 32.26 3.41
4367 4604 6.931281 CCTCATTCTCTTTCACTGTTTGACTA 59.069 38.462 0.00 0.00 32.26 2.59
4368 4605 7.605691 CCTCATTCTCTTTCACTGTTTGACTAT 59.394 37.037 0.00 0.00 32.26 2.12
4369 4606 9.645059 CTCATTCTCTTTCACTGTTTGACTATA 57.355 33.333 0.00 0.00 32.26 1.31
4469 4717 0.037326 CTGGCGGCAGTCTAGAACAA 60.037 55.000 29.42 0.00 0.00 2.83
5167 5416 4.719273 AGAGAGGCTCCTACTGCTTTAAAT 59.281 41.667 11.71 0.00 0.00 1.40
5168 5417 5.190726 AGAGAGGCTCCTACTGCTTTAAATT 59.809 40.000 11.71 0.00 0.00 1.82
5169 5418 5.821097 AGAGGCTCCTACTGCTTTAAATTT 58.179 37.500 11.71 0.00 0.00 1.82
5170 5419 6.249192 AGAGGCTCCTACTGCTTTAAATTTT 58.751 36.000 11.71 0.00 0.00 1.82
5171 5420 6.721668 AGAGGCTCCTACTGCTTTAAATTTTT 59.278 34.615 11.71 0.00 0.00 1.94
5293 6255 6.787458 TGGAGGGAAAATCATAGCATAGACTA 59.213 38.462 0.00 0.00 0.00 2.59
5294 6256 7.459125 TGGAGGGAAAATCATAGCATAGACTAT 59.541 37.037 0.00 0.00 32.99 2.12
5295 6257 8.325046 GGAGGGAAAATCATAGCATAGACTATT 58.675 37.037 0.00 0.00 30.26 1.73
5344 6306 1.598130 GTGGTGTCTCCTGGTGTGC 60.598 63.158 0.00 0.00 37.07 4.57
5521 6574 2.999063 GGGGCAAATGCTGGTGCT 60.999 61.111 5.25 0.00 40.70 4.40
5710 6763 4.638421 CCAAATCCTGCAGGTACGAATTAA 59.362 41.667 31.58 10.14 36.34 1.40
5814 6867 8.962679 AGAAGTTTACAGAGGAGTACTTCATAG 58.037 37.037 3.42 0.00 33.19 2.23
5815 6868 8.880991 AAGTTTACAGAGGAGTACTTCATAGA 57.119 34.615 3.42 0.00 0.00 1.98
5995 7048 2.949644 GTGCTGGCGGGTAAGAATTAAT 59.050 45.455 0.00 0.00 28.70 1.40
6031 7092 2.849294 TGTGCAGTTAGGCATACACA 57.151 45.000 0.00 0.00 46.92 3.72
6155 7216 3.480133 GGCCATCCAGCGGGTACT 61.480 66.667 1.81 0.00 34.93 2.73
6269 7471 8.784043 AGTTTCTTTGTTGCATTACTACTTAGG 58.216 33.333 0.00 0.00 0.00 2.69
6475 7677 3.634568 AAGACAGAAGAGTCAGTGACG 57.365 47.619 17.40 4.93 40.98 4.35
6662 7875 9.337396 TCTTTCTACTTTTTAAACAGCATCTGA 57.663 29.630 1.20 0.00 35.18 3.27
6692 7905 7.754027 TCTCTAGAATTGCTACTCGTTTTACAC 59.246 37.037 0.00 0.00 0.00 2.90
6712 7925 9.768662 TTTACACGGAAAAGATTACTTCTTAGT 57.231 29.630 0.00 0.00 44.09 2.24
6744 7957 1.013596 CCGCCGTGATATTTCAAGCA 58.986 50.000 9.18 0.00 34.56 3.91
6754 7967 7.201609 CCGTGATATTTCAAGCAAGCTACTTAA 60.202 37.037 0.00 0.00 32.48 1.85
6755 7968 8.338259 CGTGATATTTCAAGCAAGCTACTTAAT 58.662 33.333 0.00 3.11 32.48 1.40
6756 7969 9.443283 GTGATATTTCAAGCAAGCTACTTAATG 57.557 33.333 0.00 0.00 32.48 1.90
6759 7972 4.568072 TCAAGCAAGCTACTTAATGGGA 57.432 40.909 0.00 0.00 0.00 4.37
6761 7974 4.225042 TCAAGCAAGCTACTTAATGGGAGA 59.775 41.667 0.00 0.00 0.00 3.71
6762 7975 5.104360 TCAAGCAAGCTACTTAATGGGAGAT 60.104 40.000 0.00 0.00 0.00 2.75
6812 8076 6.202379 TGTGCCATTGTGAACAATAAACATTG 59.798 34.615 8.29 0.00 44.10 2.82
6833 8097 7.710044 ACATTGTTCAATTTTCTGTTATGTGCA 59.290 29.630 0.00 0.00 0.00 4.57
6837 8101 9.107177 TGTTCAATTTTCTGTTATGTGCAAAAT 57.893 25.926 0.00 0.00 0.00 1.82
6895 8159 7.096065 GGTGAAAGAAACAAATTCAATTCTCCG 60.096 37.037 9.77 0.00 38.51 4.63
6904 8168 7.363431 ACAAATTCAATTCTCCGAAAGACTTC 58.637 34.615 0.00 0.00 32.27 3.01
6976 8240 5.575957 ACGAATGTGATTTCATCATGAAGC 58.424 37.500 0.00 0.00 42.04 3.86
6978 8242 6.031471 CGAATGTGATTTCATCATGAAGCAA 58.969 36.000 0.00 0.00 42.04 3.91
6980 8244 7.305993 CGAATGTGATTTCATCATGAAGCAATG 60.306 37.037 0.00 0.00 42.04 2.82
6981 8245 6.275494 TGTGATTTCATCATGAAGCAATGT 57.725 33.333 0.00 0.00 42.04 2.71
6982 8246 6.693466 TGTGATTTCATCATGAAGCAATGTT 58.307 32.000 0.00 0.00 42.04 2.71
6983 8247 7.156000 TGTGATTTCATCATGAAGCAATGTTT 58.844 30.769 0.00 0.00 42.04 2.83
6984 8248 7.117092 TGTGATTTCATCATGAAGCAATGTTTG 59.883 33.333 0.00 0.00 42.04 2.93
6985 8249 7.117236 GTGATTTCATCATGAAGCAATGTTTGT 59.883 33.333 0.00 0.00 42.04 2.83
7007 8271 8.795786 TTGTATTTTGCTGTTCATAACAAGAC 57.204 30.769 0.00 0.00 41.61 3.01
7033 8297 7.040823 CCATTTGAGCTGGGATTAGAAGAATAC 60.041 40.741 0.00 0.00 0.00 1.89
7036 8300 7.914427 TGAGCTGGGATTAGAAGAATACTTA 57.086 36.000 0.00 0.00 36.39 2.24
7044 8308 9.495572 GGGATTAGAAGAATACTTATGACTTGG 57.504 37.037 0.00 0.00 36.39 3.61
7045 8309 9.495572 GGATTAGAAGAATACTTATGACTTGGG 57.504 37.037 0.00 0.00 36.39 4.12
7072 8336 3.739300 TCTTCTCCTTTTCTTGTTACGCG 59.261 43.478 3.53 3.53 0.00 6.01
7095 8359 3.754323 GAGCTAGATCACGCTATAGTGGT 59.246 47.826 17.34 5.60 42.10 4.16
7153 8419 3.373439 GCACTCTGCTCAAATAGAAGTGG 59.627 47.826 0.00 0.00 40.96 4.00
7173 9954 5.244626 AGTGGCACTTTGCTCAAATATTTCT 59.755 36.000 15.88 0.00 44.28 2.52
7219 10021 9.498462 GCTTATAAAAGTCTTCAGCTCGTGCTC 62.498 44.444 9.42 0.00 40.25 4.26
7227 10108 3.918220 GCTCGTGCTCGCCGATTG 61.918 66.667 2.69 0.00 36.96 2.67
7228 10109 2.507102 CTCGTGCTCGCCGATTGT 60.507 61.111 2.69 0.00 36.96 2.71
7232 10113 1.348594 GTGCTCGCCGATTGTTAGC 59.651 57.895 0.00 0.00 0.00 3.09
7263 10144 4.598257 ACGCGAGTTCCCATCTTG 57.402 55.556 15.93 0.00 46.40 3.02
7264 10145 1.079127 ACGCGAGTTCCCATCTTGG 60.079 57.895 15.93 0.00 46.40 3.61
7302 10184 0.177373 GAGACACCCGGTTGGATACC 59.823 60.000 3.27 0.00 44.03 2.73
7303 10185 0.252558 AGACACCCGGTTGGATACCT 60.253 55.000 3.27 0.00 45.40 3.08
7304 10186 0.177373 GACACCCGGTTGGATACCTC 59.823 60.000 3.27 0.00 45.40 3.85
7305 10187 1.269703 ACACCCGGTTGGATACCTCC 61.270 60.000 3.27 0.00 45.40 4.30
7391 10278 6.235231 TGTCCTACAGACTTGTTTTCTCTT 57.765 37.500 0.00 0.00 46.46 2.85
7392 10279 6.281405 TGTCCTACAGACTTGTTTTCTCTTC 58.719 40.000 0.00 0.00 46.46 2.87
7393 10280 5.402867 GTCCTACAGACTTGTTTTCTCTTCG 59.597 44.000 0.00 0.00 42.69 3.79
7394 10281 5.068723 TCCTACAGACTTGTTTTCTCTTCGT 59.931 40.000 0.00 0.00 38.76 3.85
7395 10282 5.402867 CCTACAGACTTGTTTTCTCTTCGTC 59.597 44.000 0.00 0.00 38.76 4.20
7396 10283 4.120589 ACAGACTTGTTTTCTCTTCGTCC 58.879 43.478 0.00 0.00 32.28 4.79
7397 10284 4.141914 ACAGACTTGTTTTCTCTTCGTCCT 60.142 41.667 0.00 0.00 32.28 3.85
7398 10285 5.068723 ACAGACTTGTTTTCTCTTCGTCCTA 59.931 40.000 0.00 0.00 32.28 2.94
7399 10286 6.159988 CAGACTTGTTTTCTCTTCGTCCTAT 58.840 40.000 0.00 0.00 0.00 2.57
7400 10287 6.090088 CAGACTTGTTTTCTCTTCGTCCTATG 59.910 42.308 0.00 0.00 0.00 2.23
7401 10288 4.691216 ACTTGTTTTCTCTTCGTCCTATGC 59.309 41.667 0.00 0.00 0.00 3.14
7402 10289 4.537135 TGTTTTCTCTTCGTCCTATGCT 57.463 40.909 0.00 0.00 0.00 3.79
7403 10290 4.495422 TGTTTTCTCTTCGTCCTATGCTC 58.505 43.478 0.00 0.00 0.00 4.26
7404 10291 3.422417 TTTCTCTTCGTCCTATGCTCG 57.578 47.619 0.00 0.00 0.00 5.03
7405 10292 2.327200 TCTCTTCGTCCTATGCTCGA 57.673 50.000 0.00 0.00 0.00 4.04
7406 10293 1.941294 TCTCTTCGTCCTATGCTCGAC 59.059 52.381 0.00 0.00 33.38 4.20
7407 10294 1.671328 CTCTTCGTCCTATGCTCGACA 59.329 52.381 0.00 0.00 33.38 4.35
7408 10295 2.089201 TCTTCGTCCTATGCTCGACAA 58.911 47.619 0.00 0.00 33.38 3.18
7409 10296 2.490509 TCTTCGTCCTATGCTCGACAAA 59.509 45.455 0.00 0.00 33.38 2.83
7410 10297 2.273370 TCGTCCTATGCTCGACAAAC 57.727 50.000 0.00 0.00 0.00 2.93
7411 10298 1.135199 TCGTCCTATGCTCGACAAACC 60.135 52.381 0.00 0.00 0.00 3.27
7412 10299 1.135083 CGTCCTATGCTCGACAAACCT 60.135 52.381 0.00 0.00 0.00 3.50
7413 10300 2.098607 CGTCCTATGCTCGACAAACCTA 59.901 50.000 0.00 0.00 0.00 3.08
7414 10301 3.243434 CGTCCTATGCTCGACAAACCTAT 60.243 47.826 0.00 0.00 0.00 2.57
7415 10302 4.023450 CGTCCTATGCTCGACAAACCTATA 60.023 45.833 0.00 0.00 0.00 1.31
7416 10303 5.335740 CGTCCTATGCTCGACAAACCTATAT 60.336 44.000 0.00 0.00 0.00 0.86
7417 10304 5.864474 GTCCTATGCTCGACAAACCTATATG 59.136 44.000 0.00 0.00 0.00 1.78
7418 10305 5.773176 TCCTATGCTCGACAAACCTATATGA 59.227 40.000 0.00 0.00 0.00 2.15
7419 10306 6.071896 TCCTATGCTCGACAAACCTATATGAG 60.072 42.308 0.00 0.00 0.00 2.90
7420 10307 5.537300 ATGCTCGACAAACCTATATGAGT 57.463 39.130 0.00 0.00 0.00 3.41
7421 10308 4.682787 TGCTCGACAAACCTATATGAGTG 58.317 43.478 0.00 0.00 0.00 3.51
7422 10309 3.491267 GCTCGACAAACCTATATGAGTGC 59.509 47.826 0.00 0.00 0.00 4.40
7423 10310 4.682787 CTCGACAAACCTATATGAGTGCA 58.317 43.478 0.00 0.00 0.00 4.57
7424 10311 5.276461 TCGACAAACCTATATGAGTGCAT 57.724 39.130 0.00 0.00 38.54 3.96
7425 10312 5.049828 TCGACAAACCTATATGAGTGCATG 58.950 41.667 0.00 0.00 35.94 4.06
7426 10313 4.811024 CGACAAACCTATATGAGTGCATGT 59.189 41.667 0.00 0.00 35.94 3.21
7427 10314 5.050769 CGACAAACCTATATGAGTGCATGTC 60.051 44.000 0.00 0.00 35.94 3.06
7428 10315 5.126067 ACAAACCTATATGAGTGCATGTCC 58.874 41.667 0.00 0.00 35.94 4.02
7429 10316 4.357918 AACCTATATGAGTGCATGTCCC 57.642 45.455 0.00 0.00 35.94 4.46
7430 10317 3.591789 ACCTATATGAGTGCATGTCCCT 58.408 45.455 0.00 0.00 35.94 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.120530 TCATAAACCTCCTCCTCGCC 58.879 55.000 0.00 0.00 0.00 5.54
30 31 1.474077 CTTTGCACTGGAGGGTTATGC 59.526 52.381 0.00 0.00 36.81 3.14
64 65 4.271816 CCTCGCGTCGATGAGGGG 62.272 72.222 13.22 13.22 46.55 4.79
88 89 1.135402 GCCACCCATGAATCGACAAAC 60.135 52.381 0.00 0.00 0.00 2.93
90 91 0.679640 GGCCACCCATGAATCGACAA 60.680 55.000 0.00 0.00 0.00 3.18
94 95 3.585990 GCGGCCACCCATGAATCG 61.586 66.667 2.24 0.00 0.00 3.34
126 127 2.599597 CCTCCTCCTGGCCAATGG 59.400 66.667 7.01 5.63 0.00 3.16
134 135 1.153549 GCGTTGTAGCCTCCTCCTG 60.154 63.158 0.00 0.00 0.00 3.86
136 137 1.448013 GTGCGTTGTAGCCTCCTCC 60.448 63.158 0.00 0.00 36.02 4.30
140 141 1.301401 TGTGGTGCGTTGTAGCCTC 60.301 57.895 0.00 0.00 36.02 4.70
150 151 1.665916 CCTCAGAGTGTGTGGTGCG 60.666 63.158 0.28 0.00 35.40 5.34
158 159 4.323569 TCTGACCTTATCCTCAGAGTGT 57.676 45.455 0.00 0.00 38.39 3.55
167 168 4.363991 AGCCATGAATCTGACCTTATCC 57.636 45.455 0.00 0.00 0.00 2.59
199 200 1.880340 CAACCAGATCTCGGCGAGC 60.880 63.158 31.01 18.41 0.00 5.03
202 203 2.202932 CCCAACCAGATCTCGGCG 60.203 66.667 0.00 0.00 0.00 6.46
205 206 1.135915 CACTCTCCCAACCAGATCTCG 59.864 57.143 0.00 0.00 0.00 4.04
207 208 2.630889 TCACTCTCCCAACCAGATCT 57.369 50.000 0.00 0.00 0.00 2.75
215 216 2.568956 CCTTCACTCATCACTCTCCCAA 59.431 50.000 0.00 0.00 0.00 4.12
216 217 2.182827 CCTTCACTCATCACTCTCCCA 58.817 52.381 0.00 0.00 0.00 4.37
231 232 2.158385 GCCCTATCCTCTCTCTCCTTCA 60.158 54.545 0.00 0.00 0.00 3.02
233 234 1.203001 CGCCCTATCCTCTCTCTCCTT 60.203 57.143 0.00 0.00 0.00 3.36
234 235 0.404040 CGCCCTATCCTCTCTCTCCT 59.596 60.000 0.00 0.00 0.00 3.69
237 238 0.553819 ACACGCCCTATCCTCTCTCT 59.446 55.000 0.00 0.00 0.00 3.10
239 240 0.757188 CCACACGCCCTATCCTCTCT 60.757 60.000 0.00 0.00 0.00 3.10
240 241 1.742768 CCACACGCCCTATCCTCTC 59.257 63.158 0.00 0.00 0.00 3.20
241 242 1.762460 CCCACACGCCCTATCCTCT 60.762 63.158 0.00 0.00 0.00 3.69
242 243 1.749334 CTCCCACACGCCCTATCCTC 61.749 65.000 0.00 0.00 0.00 3.71
243 244 1.762460 CTCCCACACGCCCTATCCT 60.762 63.158 0.00 0.00 0.00 3.24
245 246 1.742768 CTCTCCCACACGCCCTATC 59.257 63.158 0.00 0.00 0.00 2.08
246 247 1.762460 CCTCTCCCACACGCCCTAT 60.762 63.158 0.00 0.00 0.00 2.57
257 258 0.999712 TGACCCATTTTCCCTCTCCC 59.000 55.000 0.00 0.00 0.00 4.30
266 267 3.644966 TTATCTCGGCTGACCCATTTT 57.355 42.857 0.00 0.00 0.00 1.82
286 287 2.363406 GGGCAGCTTGGCATCCTT 60.363 61.111 10.86 0.00 45.76 3.36
290 291 4.772231 CAGGGGGCAGCTTGGCAT 62.772 66.667 10.86 0.00 45.76 4.40
305 306 1.666553 TTAGCACCCACGCGAACAG 60.667 57.895 15.93 0.03 36.85 3.16
325 361 3.242252 GCACGAATCTTAAAGCAGAGAGC 60.242 47.826 0.00 0.00 46.19 4.09
375 411 2.509964 AGATGTTTAAGGATTCCCGGCT 59.490 45.455 0.00 0.00 37.58 5.52
378 414 3.555956 CGTCAGATGTTTAAGGATTCCCG 59.444 47.826 0.00 0.00 37.58 5.14
438 478 5.020132 TGGGTTGGAGAACAAGAAAGAAAA 58.980 37.500 0.00 0.00 40.38 2.29
462 502 1.555477 CGAAAAGGTGGTTGTTGTGC 58.445 50.000 0.00 0.00 0.00 4.57
511 552 1.289830 TCCGGGGAGATACTTCCTTCA 59.710 52.381 0.00 0.00 37.40 3.02
599 656 2.355363 GGTGCTCGCGTGTACACA 60.355 61.111 26.20 5.60 34.69 3.72
614 671 2.125512 GATCTGCGTGCGGAAGGT 60.126 61.111 7.56 0.00 34.70 3.50
689 777 2.582498 GTGTCGAATCGGGAGGCG 60.582 66.667 1.76 0.00 0.00 5.52
782 871 6.671605 TCAGATAGAGATAGATGATGGAGGG 58.328 44.000 0.00 0.00 0.00 4.30
990 1080 1.520342 GAGCTTCATCGCGCCTTCT 60.520 57.895 0.00 0.00 34.40 2.85
995 1085 2.020559 CGTTGAGCTTCATCGCGC 59.979 61.111 0.00 0.00 33.63 6.86
1089 1179 5.762711 CGATTGGAGAGAGATAGAGACAAGA 59.237 44.000 0.00 0.00 0.00 3.02
1092 1182 3.818210 GCGATTGGAGAGAGATAGAGACA 59.182 47.826 0.00 0.00 0.00 3.41
1162 1253 3.211963 GCGCCCCAATAGCACCAG 61.212 66.667 0.00 0.00 0.00 4.00
1341 1432 0.725117 CACCCAGCCGACGTAAAATC 59.275 55.000 0.00 0.00 0.00 2.17
1420 1512 4.870991 GCTACAACAGATAACAGACTTCCC 59.129 45.833 0.00 0.00 0.00 3.97
1444 1537 1.964552 TTGCAGGCCCAAACAATTTG 58.035 45.000 0.00 0.00 40.32 2.32
1446 1539 2.506444 CATTTGCAGGCCCAAACAATT 58.494 42.857 9.07 0.00 37.51 2.32
1457 1550 2.734606 CACAACATCAAGCATTTGCAGG 59.265 45.455 5.20 0.00 45.16 4.85
1462 1555 4.053295 GTGAAGCACAACATCAAGCATTT 58.947 39.130 0.00 0.00 34.08 2.32
1476 1569 7.599245 ACAAACAGATTAGTACTAGTGAAGCAC 59.401 37.037 5.39 0.00 34.10 4.40
1498 1591 0.394488 TCACCCACCTGCGAAACAAA 60.394 50.000 0.00 0.00 0.00 2.83
1781 1889 2.185004 TGTCAAGCTTAGTTCCCTGC 57.815 50.000 0.00 0.00 0.00 4.85
1916 2024 7.855409 CAGACAAACATGAATACTTCGACAAAA 59.145 33.333 0.00 0.00 0.00 2.44
1918 2026 6.704050 TCAGACAAACATGAATACTTCGACAA 59.296 34.615 0.00 0.00 0.00 3.18
1957 2065 2.696707 CCATATTGGTTTGAGCAGGCAT 59.303 45.455 0.00 0.00 31.35 4.40
2121 2229 3.432252 CCAATTAGCGGGCTATAAACTCG 59.568 47.826 0.55 0.00 0.00 4.18
2128 2236 3.679389 CTTCATCCAATTAGCGGGCTAT 58.321 45.455 0.55 0.00 0.00 2.97
2347 2455 5.731957 AATTAAACACGTAGGGGCAATTT 57.268 34.783 0.00 0.00 0.00 1.82
2356 2464 6.249035 ACCATGGTCAAATTAAACACGTAG 57.751 37.500 13.00 0.00 0.00 3.51
2370 2478 5.776173 AACGAAACAAAATACCATGGTCA 57.224 34.783 23.76 8.63 0.00 4.02
2372 2480 6.399639 AGAAACGAAACAAAATACCATGGT 57.600 33.333 23.55 23.55 0.00 3.55
2460 2570 9.941325 ATTGCTGACAAAATACAAATATGGAAA 57.059 25.926 0.00 0.00 39.77 3.13
2521 2631 6.371809 ACTTTCAACGATTTAAGAAGTGCA 57.628 33.333 0.00 0.00 0.00 4.57
2536 2646 2.427095 ACTTCTGGCACCAACTTTCAAC 59.573 45.455 0.00 0.00 0.00 3.18
2539 2649 2.024414 ACACTTCTGGCACCAACTTTC 58.976 47.619 0.00 0.00 0.00 2.62
2649 2761 3.370104 AGCAGTAGAAGCACCACTAGAT 58.630 45.455 0.00 0.00 0.00 1.98
2650 2762 2.808919 AGCAGTAGAAGCACCACTAGA 58.191 47.619 0.00 0.00 0.00 2.43
2651 2763 3.056536 TGAAGCAGTAGAAGCACCACTAG 60.057 47.826 0.00 0.00 0.00 2.57
2825 3037 9.585369 TGGGAATGAAGATGCATATAAAATACA 57.415 29.630 0.00 0.00 0.00 2.29
2826 3038 9.846248 GTGGGAATGAAGATGCATATAAAATAC 57.154 33.333 0.00 0.00 0.00 1.89
2827 3039 9.023962 GGTGGGAATGAAGATGCATATAAAATA 57.976 33.333 0.00 0.00 0.00 1.40
2828 3040 7.731688 AGGTGGGAATGAAGATGCATATAAAAT 59.268 33.333 0.00 0.00 0.00 1.82
2829 3041 7.068702 AGGTGGGAATGAAGATGCATATAAAA 58.931 34.615 0.00 0.00 0.00 1.52
2830 3042 6.613699 AGGTGGGAATGAAGATGCATATAAA 58.386 36.000 0.00 0.00 0.00 1.40
2831 3043 6.204852 AGGTGGGAATGAAGATGCATATAA 57.795 37.500 0.00 0.00 0.00 0.98
2832 3044 5.848286 AGGTGGGAATGAAGATGCATATA 57.152 39.130 0.00 0.00 0.00 0.86
2833 3045 4.736611 AGGTGGGAATGAAGATGCATAT 57.263 40.909 0.00 0.00 0.00 1.78
2903 3115 8.387813 AGAGTCCACATATAACCCTAACAAAAA 58.612 33.333 0.00 0.00 0.00 1.94
3096 3316 4.277476 TGAGGGTCACACAGAAACAAAAT 58.723 39.130 0.00 0.00 0.00 1.82
3413 3633 6.722129 GGAGGGAGTAGCTTCTAATAGAATGA 59.278 42.308 2.87 0.00 33.13 2.57
3449 3669 9.204570 AGCATATTGGATGTAATAACGTCTTAC 57.795 33.333 11.92 11.92 40.82 2.34
3478 3698 4.080582 CCCGCCATCCCATAATATAAGACA 60.081 45.833 0.00 0.00 0.00 3.41
3495 3715 4.412843 TCAGTATCAATATACTCCCGCCA 58.587 43.478 0.00 0.00 44.05 5.69
3584 3804 5.192927 CCATATGACAAGGCAAGTAAGGAA 58.807 41.667 3.65 0.00 0.00 3.36
3585 3805 4.227300 ACCATATGACAAGGCAAGTAAGGA 59.773 41.667 3.65 0.00 0.00 3.36
3586 3806 4.526970 ACCATATGACAAGGCAAGTAAGG 58.473 43.478 3.65 0.00 0.00 2.69
3587 3807 4.271049 CGACCATATGACAAGGCAAGTAAG 59.729 45.833 3.65 0.00 0.00 2.34
3590 3810 2.632377 CGACCATATGACAAGGCAAGT 58.368 47.619 3.65 0.00 0.00 3.16
3599 3823 3.001634 CACATGACAAGCGACCATATGAC 59.998 47.826 3.65 0.00 0.00 3.06
3668 3894 2.670019 AAACCAGTACAAGTTCCCCC 57.330 50.000 0.00 0.00 0.00 5.40
3827 4053 5.395214 GGCTCCAGTTCAAAAAGAAAAAGGA 60.395 40.000 0.00 0.00 38.13 3.36
3844 4070 6.704289 TTCAAGAATAATTCATGGCTCCAG 57.296 37.500 0.00 0.00 0.00 3.86
3852 4078 8.529424 TTCTCAGGCATTCAAGAATAATTCAT 57.471 30.769 0.00 0.00 0.00 2.57
3857 4083 7.361201 CGTTTCTTCTCAGGCATTCAAGAATAA 60.361 37.037 0.00 0.00 34.03 1.40
3946 4172 2.493675 TGACTTGTCAGCTGCTAGGTAG 59.506 50.000 9.47 2.93 0.00 3.18
4092 4318 7.747690 TCTTTAACTTTTGTCCAGTATACCCA 58.252 34.615 0.00 0.00 0.00 4.51
4093 4319 8.625786 TTCTTTAACTTTTGTCCAGTATACCC 57.374 34.615 0.00 0.00 0.00 3.69
4098 4324 9.621629 TCATCTTTCTTTAACTTTTGTCCAGTA 57.378 29.630 0.00 0.00 0.00 2.74
4099 4325 8.519799 TCATCTTTCTTTAACTTTTGTCCAGT 57.480 30.769 0.00 0.00 0.00 4.00
4100 4326 9.971922 ATTCATCTTTCTTTAACTTTTGTCCAG 57.028 29.630 0.00 0.00 0.00 3.86
4177 4414 7.652909 TCCACACATTCAGAAAATAAAGCAAAG 59.347 33.333 0.00 0.00 0.00 2.77
4201 4438 3.130340 TGAACTGCCAGTTTTTGAAGTCC 59.870 43.478 12.09 0.00 38.80 3.85
4469 4717 3.697045 TGTCAAGAATTTGTTGGACCGTT 59.303 39.130 6.45 0.00 35.73 4.44
5056 5305 1.032014 AAATGAAGTTGCGGCAGTGT 58.968 45.000 1.67 0.00 0.00 3.55
5134 5383 1.675415 GGAGCCTCTCTTGCTGTGAAG 60.675 57.143 0.00 0.00 39.69 3.02
5135 5384 0.322975 GGAGCCTCTCTTGCTGTGAA 59.677 55.000 0.00 0.00 39.69 3.18
5136 5385 0.543883 AGGAGCCTCTCTTGCTGTGA 60.544 55.000 0.00 0.00 39.69 3.58
5137 5386 1.134848 GTAGGAGCCTCTCTTGCTGTG 60.135 57.143 0.00 0.00 39.69 3.66
5138 5387 1.190643 GTAGGAGCCTCTCTTGCTGT 58.809 55.000 0.00 0.00 39.69 4.40
5293 6255 9.319143 GACAGTTGTAAGAGCATATCTAACAAT 57.681 33.333 0.00 0.00 37.23 2.71
5294 6256 8.531982 AGACAGTTGTAAGAGCATATCTAACAA 58.468 33.333 0.00 0.00 37.23 2.83
5295 6257 7.976175 CAGACAGTTGTAAGAGCATATCTAACA 59.024 37.037 0.00 0.00 37.23 2.41
5344 6306 5.675575 GCATAATGCTTTGTCAAGGAGACTG 60.676 44.000 0.00 0.00 43.26 3.51
5542 6595 2.278336 CGCAATGCATCAAGGGCG 60.278 61.111 5.91 7.43 38.45 6.13
5592 6645 4.787551 ACACTTCAATGACCAACCAGTAA 58.212 39.130 0.00 0.00 0.00 2.24
5710 6763 9.536510 TTTGCATAGGGTACTAAATAAAAAGGT 57.463 29.630 0.00 0.00 31.86 3.50
5769 6822 8.754230 AACTTCTATAAGACGTTTTAGGTCAC 57.246 34.615 4.75 0.00 33.60 3.67
5776 6829 9.420551 CCTCTGTAAACTTCTATAAGACGTTTT 57.579 33.333 14.29 0.00 41.88 2.43
5778 6831 8.345724 TCCTCTGTAAACTTCTATAAGACGTT 57.654 34.615 0.00 0.00 38.18 3.99
6031 7092 6.160576 AGAAAACACCAATGTAAATGCTGT 57.839 33.333 0.00 0.00 38.45 4.40
6475 7677 2.548480 GACACCAAACTGTACTGCTTCC 59.452 50.000 0.00 0.00 0.00 3.46
6664 7877 9.947669 GTAAAACGAGTAGCAATTCTAGAGATA 57.052 33.333 0.00 0.00 0.00 1.98
6728 7941 4.572389 AGTAGCTTGCTTGAAATATCACGG 59.428 41.667 0.00 0.00 34.61 4.94
6744 7957 4.971924 ACTCCATCTCCCATTAAGTAGCTT 59.028 41.667 0.00 0.00 0.00 3.74
6762 7975 1.490490 AGCTTGAGTGTGGAAACTCCA 59.510 47.619 2.12 0.00 45.98 3.86
6812 8076 9.934190 AATTTTGCACATAACAGAAAATTGAAC 57.066 25.926 0.00 0.00 35.77 3.18
6867 8131 8.652810 AGAATTGAATTTGTTTCTTTCACCTG 57.347 30.769 0.00 0.00 35.23 4.00
6868 8132 7.928167 GGAGAATTGAATTTGTTTCTTTCACCT 59.072 33.333 0.00 0.00 36.36 4.00
6895 8159 8.713271 CACCAAAATACTGTAGAGAAGTCTTTC 58.287 37.037 0.00 0.00 33.84 2.62
6904 8168 7.672983 ATCAACACACCAAAATACTGTAGAG 57.327 36.000 0.00 0.00 0.00 2.43
6941 8205 1.066143 CACATTCGTGGAGGCCTAAGT 60.066 52.381 4.42 0.00 39.64 2.24
6975 8239 6.284475 TGAACAGCAAAATACAAACATTGC 57.716 33.333 1.31 1.31 46.43 3.56
6976 8240 9.796062 GTTATGAACAGCAAAATACAAACATTG 57.204 29.630 0.00 0.00 0.00 2.82
6978 8242 9.539825 TTGTTATGAACAGCAAAATACAAACAT 57.460 25.926 0.00 0.00 43.27 2.71
6980 8244 9.243637 TCTTGTTATGAACAGCAAAATACAAAC 57.756 29.630 0.00 0.00 43.27 2.93
6981 8245 9.243637 GTCTTGTTATGAACAGCAAAATACAAA 57.756 29.630 0.00 0.00 43.27 2.83
6982 8246 7.865385 GGTCTTGTTATGAACAGCAAAATACAA 59.135 33.333 0.00 0.00 43.27 2.41
6983 8247 7.013750 TGGTCTTGTTATGAACAGCAAAATACA 59.986 33.333 0.00 0.00 43.27 2.29
6984 8248 7.367285 TGGTCTTGTTATGAACAGCAAAATAC 58.633 34.615 0.00 0.00 43.27 1.89
6985 8249 7.517614 TGGTCTTGTTATGAACAGCAAAATA 57.482 32.000 0.00 0.00 43.27 1.40
7007 8271 4.785301 TCTTCTAATCCCAGCTCAAATGG 58.215 43.478 0.00 0.00 37.58 3.16
7033 8297 7.569240 AGGAGAAGATAAACCCAAGTCATAAG 58.431 38.462 0.00 0.00 0.00 1.73
7036 8300 6.394345 AAGGAGAAGATAAACCCAAGTCAT 57.606 37.500 0.00 0.00 0.00 3.06
7043 8307 7.526142 AACAAGAAAAGGAGAAGATAAACCC 57.474 36.000 0.00 0.00 0.00 4.11
7044 8308 8.228464 CGTAACAAGAAAAGGAGAAGATAAACC 58.772 37.037 0.00 0.00 0.00 3.27
7045 8309 7.745155 GCGTAACAAGAAAAGGAGAAGATAAAC 59.255 37.037 0.00 0.00 0.00 2.01
7072 8336 3.127895 CCACTATAGCGTGATCTAGCTCC 59.872 52.174 16.58 0.00 43.44 4.70
7079 8343 3.710326 TGTGACCACTATAGCGTGATC 57.290 47.619 0.00 0.00 37.06 2.92
7083 8347 6.644248 TGTAATATGTGACCACTATAGCGT 57.356 37.500 0.00 0.00 0.00 5.07
7136 8402 3.341823 AGTGCCACTTCTATTTGAGCAG 58.658 45.455 0.00 0.00 0.00 4.24
7146 8412 2.057137 TTGAGCAAAGTGCCACTTCT 57.943 45.000 11.11 4.44 46.52 2.85
7147 8413 2.869233 TTTGAGCAAAGTGCCACTTC 57.131 45.000 11.11 0.00 46.52 3.01
7149 8415 5.244626 AGAAATATTTGAGCAAAGTGCCACT 59.755 36.000 5.17 0.00 46.52 4.00
7153 8419 6.615088 TCTCAGAAATATTTGAGCAAAGTGC 58.385 36.000 5.17 0.00 45.46 4.40
7173 9954 4.026744 AGCAAATCTAGCACCTACTCTCA 58.973 43.478 0.00 0.00 0.00 3.27
7219 10021 2.221055 GGATAAGTGCTAACAATCGGCG 59.779 50.000 0.00 0.00 0.00 6.46
7220 10022 3.202906 TGGATAAGTGCTAACAATCGGC 58.797 45.455 0.00 0.00 0.00 5.54
7221 10023 4.816385 ACATGGATAAGTGCTAACAATCGG 59.184 41.667 0.00 0.00 0.00 4.18
7227 10108 3.001330 GCGTCACATGGATAAGTGCTAAC 59.999 47.826 0.00 0.00 35.76 2.34
7228 10109 3.194861 GCGTCACATGGATAAGTGCTAA 58.805 45.455 0.00 0.00 35.76 3.09
7232 10113 1.854743 CTCGCGTCACATGGATAAGTG 59.145 52.381 5.77 0.00 37.10 3.16
7261 10142 1.395826 CCGGGTGGCAAAGAAACCAA 61.396 55.000 0.00 0.00 37.79 3.67
7262 10143 1.830408 CCGGGTGGCAAAGAAACCA 60.830 57.895 0.00 0.00 35.56 3.67
7263 10144 1.529713 TCCGGGTGGCAAAGAAACC 60.530 57.895 0.00 0.00 34.14 3.27
7264 10145 1.658114 GTCCGGGTGGCAAAGAAAC 59.342 57.895 0.00 0.00 34.14 2.78
7303 10185 9.747898 ACTATGACCTGTATTTGTAATTTTGGA 57.252 29.630 0.00 0.00 0.00 3.53
7311 10193 9.142515 CGTAACAAACTATGACCTGTATTTGTA 57.857 33.333 0.00 0.00 38.86 2.41
7312 10194 7.874016 TCGTAACAAACTATGACCTGTATTTGT 59.126 33.333 0.00 0.00 40.89 2.83
7313 10195 8.166706 GTCGTAACAAACTATGACCTGTATTTG 58.833 37.037 0.00 0.00 33.44 2.32
7391 10278 1.135199 GGTTTGTCGAGCATAGGACGA 60.135 52.381 0.00 0.00 35.95 4.20
7392 10279 1.135083 AGGTTTGTCGAGCATAGGACG 60.135 52.381 0.00 0.00 35.95 4.79
7393 10280 2.674796 AGGTTTGTCGAGCATAGGAC 57.325 50.000 0.00 0.00 0.00 3.85
7394 10281 5.773176 TCATATAGGTTTGTCGAGCATAGGA 59.227 40.000 0.00 0.00 0.00 2.94
7395 10282 6.025749 TCATATAGGTTTGTCGAGCATAGG 57.974 41.667 0.00 0.00 0.00 2.57
7396 10283 6.584184 CACTCATATAGGTTTGTCGAGCATAG 59.416 42.308 0.00 0.00 0.00 2.23
7397 10284 6.447162 CACTCATATAGGTTTGTCGAGCATA 58.553 40.000 0.00 0.00 0.00 3.14
7398 10285 5.292765 CACTCATATAGGTTTGTCGAGCAT 58.707 41.667 0.00 0.00 0.00 3.79
7399 10286 4.682787 CACTCATATAGGTTTGTCGAGCA 58.317 43.478 0.00 0.00 0.00 4.26
7400 10287 3.491267 GCACTCATATAGGTTTGTCGAGC 59.509 47.826 0.00 0.00 0.00 5.03
7401 10288 4.682787 TGCACTCATATAGGTTTGTCGAG 58.317 43.478 0.00 0.00 0.00 4.04
7402 10289 4.729227 TGCACTCATATAGGTTTGTCGA 57.271 40.909 0.00 0.00 0.00 4.20
7403 10290 4.811024 ACATGCACTCATATAGGTTTGTCG 59.189 41.667 0.00 0.00 0.00 4.35
7404 10291 5.237344 GGACATGCACTCATATAGGTTTGTC 59.763 44.000 0.00 0.00 0.00 3.18
7405 10292 5.126067 GGACATGCACTCATATAGGTTTGT 58.874 41.667 0.00 0.00 0.00 2.83
7406 10293 4.516698 GGGACATGCACTCATATAGGTTTG 59.483 45.833 0.00 0.00 0.00 2.93
7407 10294 4.413520 AGGGACATGCACTCATATAGGTTT 59.586 41.667 0.00 0.00 0.00 3.27
7408 10295 3.976654 AGGGACATGCACTCATATAGGTT 59.023 43.478 0.00 0.00 0.00 3.50
7409 10296 3.591789 AGGGACATGCACTCATATAGGT 58.408 45.455 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.