Multiple sequence alignment - TraesCS2D01G174200

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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 TraesCS2D01G174200 chr2D 100.000 4313 0 0 1 4313 117832641 117828329 0.000000e+00 7965.0
1 TraesCS2D01G174200 chr2D 82.692 156 24 3 1999 2153 621477708 621477861 7.520000e-28 135.0
2 TraesCS2D01G174200 chr2A 87.516 2315 133 66 16 2292 119080790 119078594 0.000000e+00 2531.0
3 TraesCS2D01G174200 chr2A 88.318 428 31 6 2314 2730 119078473 119078054 3.000000e-136 496.0
4 TraesCS2D01G174200 chr2B 91.227 1459 65 24 2175 3610 168611034 168609616 0.000000e+00 1927.0
5 TraesCS2D01G174200 chr2B 87.306 1158 85 31 881 2004 168612193 168611064 0.000000e+00 1267.0
6 TraesCS2D01G174200 chr2B 94.282 717 31 4 3597 4313 168608176 168607470 0.000000e+00 1088.0
7 TraesCS2D01G174200 chr2B 86.607 560 36 18 284 831 168612741 168612209 2.240000e-162 582.0
8 TraesCS2D01G174200 chr2B 95.349 172 7 1 58 228 168614117 168613946 5.500000e-69 272.0
9 TraesCS2D01G174200 chr2B 83.333 150 22 3 2008 2157 14453559 14453705 7.520000e-28 135.0
10 TraesCS2D01G174200 chr2B 83.333 150 22 3 2008 2157 14482035 14482181 7.520000e-28 135.0
11 TraesCS2D01G174200 chr2B 83.333 150 22 3 2008 2157 14508616 14508762 7.520000e-28 135.0
12 TraesCS2D01G174200 chr2B 98.413 63 1 0 3607 3669 168608275 168608213 1.270000e-20 111.0
13 TraesCS2D01G174200 chr2B 100.000 34 0 0 12 45 168614149 168614116 3.600000e-06 63.9
14 TraesCS2D01G174200 chr3A 86.864 236 12 6 3223 3445 379834460 379834231 3.330000e-61 246.0
15 TraesCS2D01G174200 chr3A 78.788 198 37 3 4120 4313 201529701 201529897 1.260000e-25 128.0
16 TraesCS2D01G174200 chr3A 84.906 106 13 3 3929 4032 158692124 158692228 2.120000e-18 104.0
17 TraesCS2D01G174200 chr6D 75.221 452 91 19 3796 4236 276133657 276134098 1.220000e-45 195.0
18 TraesCS2D01G174200 chrUn 83.333 150 22 3 2008 2157 439522416 439522562 7.520000e-28 135.0
19 TraesCS2D01G174200 chr5D 82.166 157 25 3 2002 2158 374654420 374654573 9.730000e-27 132.0
20 TraesCS2D01G174200 chr1A 82.237 152 24 2 2008 2159 531984910 531984762 1.260000e-25 128.0
21 TraesCS2D01G174200 chr1D 81.699 153 22 4 2008 2159 14748411 14748264 5.860000e-24 122.0
22 TraesCS2D01G174200 chr1B 80.667 150 26 2 2008 2157 279915643 279915497 3.530000e-21 113.0
23 TraesCS2D01G174200 chr7D 80.822 146 15 7 4169 4313 475367753 475367886 7.630000e-18 102.0
24 TraesCS2D01G174200 chr6B 73.846 260 46 19 3789 4040 604063810 604063565 2.760000e-12 84.2
25 TraesCS2D01G174200 chr3B 73.333 210 39 15 3831 4033 60370214 60370413 1.300000e-05 62.1
26 TraesCS2D01G174200 chr5B 96.970 33 1 0 3630 3662 144856118 144856150 6.030000e-04 56.5
27 TraesCS2D01G174200 chr5A 100.000 29 0 0 3985 4013 19654783 19654811 2.000000e-03 54.7


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 TraesCS2D01G174200 chr2D 117828329 117832641 4312 True 7965.0 7965 100.000 1 4313 1 chr2D.!!$R1 4312
1 TraesCS2D01G174200 chr2A 119078054 119080790 2736 True 1513.5 2531 87.917 16 2730 2 chr2A.!!$R1 2714
2 TraesCS2D01G174200 chr2B 168607470 168614149 6679 True 758.7 1927 93.312 12 4313 7 chr2B.!!$R1 4301

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
816 1990 0.453282 CGATCGCAGGCACACAAAAG 60.453 55.0 0.26 0.0 0.00 2.27 F
2309 3550 0.038744 AATCACCCTGCCAGTCCTTG 59.961 55.0 0.00 0.0 0.00 3.61 F
2755 4101 0.398522 ACCGAGGATGGTGATGGCTA 60.399 55.0 0.00 0.0 41.85 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 4091 0.179000 CCAGTGAGGTAGCCATCACC 59.821 60.0 9.87 0.00 45.61 4.02 R
3219 4566 0.108992 TTAACACGAGCTACCAGCCG 60.109 55.0 0.00 7.27 43.77 5.52 R
4072 6890 0.260230 TTTGGTGTGGTGGACATGGT 59.740 50.0 0.00 0.00 36.78 3.55 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
53 54 0.827507 CACAGGGGGTGGTCTTTTGG 60.828 60.000 0.00 0.00 44.04 3.28
112 113 9.755064 ATTTCTTCTTGTATTTATGTTTCGACG 57.245 29.630 0.00 0.00 0.00 5.12
140 149 4.111577 ACTTCTTCCCCAGATCCATTGTA 58.888 43.478 0.00 0.00 0.00 2.41
243 283 9.845740 ACAAAGTTTTAGCCAATATTTCCTTTT 57.154 25.926 0.00 0.00 0.00 2.27
260 300 3.492313 CTTTTGCGAGATGGTACTTTGC 58.508 45.455 0.00 0.00 0.00 3.68
292 1454 4.498323 GCGAGGAAGCGTATAATATTACGG 59.502 45.833 11.62 0.28 43.92 4.02
322 1484 9.754382 AATTTGTATTGCTATATGAAAAGCTGG 57.246 29.630 0.00 0.00 39.53 4.85
356 1524 7.446769 TGGTAGTAGTACATTGTTTCACATGT 58.553 34.615 9.89 0.00 0.00 3.21
375 1543 7.249186 ACATGTGTGATTGAAATGGTTTTTG 57.751 32.000 0.00 0.00 0.00 2.44
387 1555 1.960689 TGGTTTTTGCTTAGAGGTGGC 59.039 47.619 0.00 0.00 0.00 5.01
429 1603 7.315890 TGCATTATACTACTACTAGCTGCATG 58.684 38.462 1.02 0.00 31.57 4.06
435 1609 6.582677 ACTACTACTAGCTGCATGGATTAG 57.417 41.667 1.02 0.00 0.00 1.73
439 1613 4.348863 ACTAGCTGCATGGATTAGAAGG 57.651 45.455 1.02 0.00 0.00 3.46
450 1624 7.665559 TGCATGGATTAGAAGGGTGTATTATTC 59.334 37.037 0.00 0.00 0.00 1.75
500 1674 4.742201 CTGGTCGAGCCACCCACG 62.742 72.222 12.85 0.00 43.61 4.94
633 1807 1.495878 CATCTTCCTCGCCGATCTTG 58.504 55.000 0.00 0.00 0.00 3.02
724 1898 1.133025 CAGCCGAAACCCATGATGAAC 59.867 52.381 0.00 0.00 0.00 3.18
745 1919 4.234550 ACCATGGATAGAACTGGATAGCA 58.765 43.478 21.47 0.00 32.92 3.49
753 1927 3.561143 AGAACTGGATAGCAGTCGATCT 58.439 45.455 0.00 0.00 31.67 2.75
754 1928 3.957497 AGAACTGGATAGCAGTCGATCTT 59.043 43.478 0.00 0.00 31.67 2.40
755 1929 4.037446 AGAACTGGATAGCAGTCGATCTTC 59.963 45.833 0.00 0.00 31.67 2.87
757 1931 2.625314 CTGGATAGCAGTCGATCTTCCA 59.375 50.000 0.00 0.00 0.00 3.53
758 1932 2.625314 TGGATAGCAGTCGATCTTCCAG 59.375 50.000 0.00 0.00 0.00 3.86
759 1933 2.625790 GGATAGCAGTCGATCTTCCAGT 59.374 50.000 0.00 0.00 0.00 4.00
761 1935 1.846007 AGCAGTCGATCTTCCAGTCT 58.154 50.000 0.00 0.00 0.00 3.24
790 1964 5.432885 AATAGTCACCGAAACAAAACCAG 57.567 39.130 0.00 0.00 0.00 4.00
792 1966 2.943033 AGTCACCGAAACAAAACCAGAG 59.057 45.455 0.00 0.00 0.00 3.35
804 1978 4.519437 CCAGAGCAGGCGATCGCA 62.519 66.667 38.00 0.00 44.11 5.10
805 1979 2.960659 CAGAGCAGGCGATCGCAG 60.961 66.667 38.00 29.80 44.11 5.18
813 1987 3.422303 GCGATCGCAGGCACACAA 61.422 61.111 33.89 0.00 41.49 3.33
816 1990 0.453282 CGATCGCAGGCACACAAAAG 60.453 55.000 0.26 0.00 0.00 2.27
817 1991 0.730494 GATCGCAGGCACACAAAAGC 60.730 55.000 0.00 0.00 0.00 3.51
841 2019 1.421382 CTTTCCAAAATGCACCAGCG 58.579 50.000 0.00 0.00 46.23 5.18
843 2021 1.610363 TTCCAAAATGCACCAGCGTA 58.390 45.000 0.00 0.00 46.23 4.42
855 2033 3.181520 GCACCAGCGTACTTAAACATCTG 60.182 47.826 0.00 0.00 0.00 2.90
944 2129 8.401490 AGGATCAAAAAGATGGCATAGAATAC 57.599 34.615 0.00 0.00 37.00 1.89
945 2130 8.000709 AGGATCAAAAAGATGGCATAGAATACA 58.999 33.333 0.00 0.00 37.00 2.29
946 2131 8.800332 GGATCAAAAAGATGGCATAGAATACAT 58.200 33.333 0.00 0.00 37.00 2.29
971 2156 2.281761 ACAAGTTGCTGCCGGGAG 60.282 61.111 20.23 20.23 0.00 4.30
1051 2242 5.308825 ACCATCGACCAGAAAATATCATCC 58.691 41.667 0.00 0.00 0.00 3.51
1103 2298 6.542370 TCCAAAGTCTTTCTTCTTTGTACCAG 59.458 38.462 13.84 0.00 44.91 4.00
1140 2335 1.138069 TCTGAAAATATCTCGGCCGCA 59.862 47.619 23.51 10.15 0.00 5.69
1146 2344 0.826256 ATATCTCGGCCGCAGTACCA 60.826 55.000 23.51 0.00 0.00 3.25
1148 2346 2.369257 ATCTCGGCCGCAGTACCATG 62.369 60.000 23.51 1.58 0.00 3.66
1209 2415 4.785512 CAGCGCGGCGAGACTCTT 62.786 66.667 28.54 0.00 0.00 2.85
1212 2418 4.116328 CGCGGCGAGACTCTTCCA 62.116 66.667 19.16 0.00 0.00 3.53
1213 2419 2.507324 GCGGCGAGACTCTTCCAC 60.507 66.667 12.98 0.00 0.00 4.02
1215 2421 2.344203 CGGCGAGACTCTTCCACCT 61.344 63.158 0.00 0.00 0.00 4.00
1216 2422 1.216710 GGCGAGACTCTTCCACCTG 59.783 63.158 0.03 0.00 0.00 4.00
1217 2423 1.446966 GCGAGACTCTTCCACCTGC 60.447 63.158 0.03 0.00 0.00 4.85
1262 2471 1.375013 CGGATATTTACCGCCCCCG 60.375 63.158 0.00 0.00 43.74 5.73
1263 2472 1.818959 CGGATATTTACCGCCCCCGA 61.819 60.000 0.00 0.00 43.74 5.14
1264 2473 0.397564 GGATATTTACCGCCCCCGAA 59.602 55.000 0.00 0.00 36.29 4.30
1265 2474 1.003928 GGATATTTACCGCCCCCGAAT 59.996 52.381 0.00 0.00 36.29 3.34
1307 2519 5.631992 GCCACGAAGGAAATAAAAGAGAAG 58.368 41.667 2.86 0.00 41.22 2.85
1309 2521 5.181245 CCACGAAGGAAATAAAAGAGAAGCA 59.819 40.000 0.00 0.00 41.22 3.91
1310 2522 6.310197 CACGAAGGAAATAAAAGAGAAGCAG 58.690 40.000 0.00 0.00 0.00 4.24
1311 2523 5.106515 ACGAAGGAAATAAAAGAGAAGCAGC 60.107 40.000 0.00 0.00 0.00 5.25
1312 2524 4.954092 AGGAAATAAAAGAGAAGCAGCG 57.046 40.909 0.00 0.00 0.00 5.18
1313 2525 3.691609 AGGAAATAAAAGAGAAGCAGCGG 59.308 43.478 0.00 0.00 0.00 5.52
1316 2528 1.710013 TAAAAGAGAAGCAGCGGTCG 58.290 50.000 0.00 0.00 0.00 4.79
1344 2556 2.664851 CGGAACAGCACGGAAGCA 60.665 61.111 0.00 0.00 36.85 3.91
1345 2557 2.671177 CGGAACAGCACGGAAGCAG 61.671 63.158 0.00 0.00 36.85 4.24
1346 2558 2.328099 GGAACAGCACGGAAGCAGG 61.328 63.158 0.00 0.00 36.85 4.85
1347 2559 2.970974 GAACAGCACGGAAGCAGGC 61.971 63.158 0.00 0.00 36.85 4.85
1348 2560 3.772853 AACAGCACGGAAGCAGGCA 62.773 57.895 0.00 0.00 36.85 4.75
1349 2561 3.429141 CAGCACGGAAGCAGGCAG 61.429 66.667 0.00 0.00 36.85 4.85
1350 2562 4.711949 AGCACGGAAGCAGGCAGG 62.712 66.667 0.00 0.00 36.85 4.85
1412 2635 4.783763 TCTCTCTCTCTCTGGTTGGTAGTA 59.216 45.833 0.00 0.00 0.00 1.82
1413 2636 4.846040 TCTCTCTCTCTGGTTGGTAGTAC 58.154 47.826 0.00 0.00 0.00 2.73
1414 2637 4.288887 TCTCTCTCTCTGGTTGGTAGTACA 59.711 45.833 2.06 0.00 0.00 2.90
1514 2738 3.060098 GCGTTCTCTTCTTCATCGTCTTG 59.940 47.826 0.00 0.00 0.00 3.02
1522 2746 0.389817 TTCATCGTCTTGCCCGTCTG 60.390 55.000 0.00 0.00 0.00 3.51
1526 2750 2.317609 CGTCTTGCCCGTCTGGTTG 61.318 63.158 0.00 0.00 36.04 3.77
1544 2768 2.332654 GCCTGCGGATTTGTTCGGT 61.333 57.895 0.00 0.00 0.00 4.69
1546 2770 0.109781 CCTGCGGATTTGTTCGGTTG 60.110 55.000 0.00 0.00 0.00 3.77
1550 2774 1.268845 GCGGATTTGTTCGGTTGTTGT 60.269 47.619 0.00 0.00 0.00 3.32
1552 2776 2.032302 CGGATTTGTTCGGTTGTTGTGA 59.968 45.455 0.00 0.00 0.00 3.58
1800 3024 2.966309 GCAAAGGTTGAGCGGACCG 61.966 63.158 10.29 10.29 42.11 4.79
1899 3129 1.112916 TGAGACCGTGCAAGAGTCCA 61.113 55.000 14.28 10.66 0.00 4.02
1989 3219 1.472878 CTTCTAGCACTGCAGGTACGA 59.527 52.381 19.93 4.81 0.00 3.43
2006 3236 2.359900 ACGATGTTCCTCAAAGATGCC 58.640 47.619 0.00 0.00 0.00 4.40
2030 3260 6.263842 CCCCCTCCGTTTTTAAATATAAGACC 59.736 42.308 0.00 0.00 0.00 3.85
2108 3338 6.305693 AGTGTACATTCACTCTTTTTGCTC 57.694 37.500 0.00 0.00 44.07 4.26
2109 3339 5.239525 AGTGTACATTCACTCTTTTTGCTCC 59.760 40.000 0.00 0.00 44.07 4.70
2110 3340 3.904136 ACATTCACTCTTTTTGCTCCG 57.096 42.857 0.00 0.00 0.00 4.63
2111 3341 3.214328 ACATTCACTCTTTTTGCTCCGT 58.786 40.909 0.00 0.00 0.00 4.69
2115 3345 6.092259 ACATTCACTCTTTTTGCTCCGTATAC 59.908 38.462 0.00 0.00 0.00 1.47
2118 3348 4.929808 CACTCTTTTTGCTCCGTATACAGT 59.070 41.667 3.32 0.00 0.00 3.55
2130 3360 6.755141 GCTCCGTATACAGTCTGTATTGAAAA 59.245 38.462 26.52 9.14 40.40 2.29
2131 3361 7.438459 GCTCCGTATACAGTCTGTATTGAAAAT 59.562 37.037 26.52 8.76 40.40 1.82
2132 3362 8.867112 TCCGTATACAGTCTGTATTGAAAATC 57.133 34.615 26.52 10.58 40.40 2.17
2133 3363 8.692710 TCCGTATACAGTCTGTATTGAAAATCT 58.307 33.333 26.52 6.52 40.40 2.40
2134 3364 8.969267 CCGTATACAGTCTGTATTGAAAATCTC 58.031 37.037 26.52 8.75 40.40 2.75
2135 3365 9.737427 CGTATACAGTCTGTATTGAAAATCTCT 57.263 33.333 26.52 5.40 40.40 3.10
2258 3492 9.461312 TCAGCTATGTGTTTTACCAAGAATAAT 57.539 29.630 0.00 0.00 0.00 1.28
2307 3548 1.668826 TAAATCACCCTGCCAGTCCT 58.331 50.000 0.00 0.00 0.00 3.85
2309 3550 0.038744 AATCACCCTGCCAGTCCTTG 59.961 55.000 0.00 0.00 0.00 3.61
2310 3551 1.136329 ATCACCCTGCCAGTCCTTGT 61.136 55.000 0.00 0.00 0.00 3.16
2313 3554 0.620556 ACCCTGCCAGTCCTTGTATG 59.379 55.000 0.00 0.00 0.00 2.39
2314 3555 0.620556 CCCTGCCAGTCCTTGTATGT 59.379 55.000 0.00 0.00 0.00 2.29
2315 3556 1.837439 CCCTGCCAGTCCTTGTATGTA 59.163 52.381 0.00 0.00 0.00 2.29
2317 3558 2.555199 CTGCCAGTCCTTGTATGTAGC 58.445 52.381 0.00 0.00 0.00 3.58
2319 3560 2.093500 TGCCAGTCCTTGTATGTAGCAG 60.093 50.000 0.00 0.00 0.00 4.24
2320 3561 2.555199 CCAGTCCTTGTATGTAGCAGC 58.445 52.381 0.00 0.00 0.00 5.25
2321 3562 2.196749 CAGTCCTTGTATGTAGCAGCG 58.803 52.381 0.00 0.00 0.00 5.18
2323 3564 0.534873 TCCTTGTATGTAGCAGCGCA 59.465 50.000 11.47 0.00 0.00 6.09
2447 3792 6.122964 GGCAAGATTCTTACAAGGGAACTAT 58.877 40.000 0.00 0.00 42.68 2.12
2486 3831 2.092914 GGGGTCGGATCAGAACTTCATT 60.093 50.000 10.82 0.00 0.00 2.57
2497 3842 6.471233 TCAGAACTTCATTGACGAGGATAT 57.529 37.500 0.00 0.00 0.00 1.63
2498 3843 7.582667 TCAGAACTTCATTGACGAGGATATA 57.417 36.000 0.00 0.00 0.00 0.86
2499 3844 8.183104 TCAGAACTTCATTGACGAGGATATAT 57.817 34.615 0.00 0.00 0.00 0.86
2500 3845 9.297037 TCAGAACTTCATTGACGAGGATATATA 57.703 33.333 0.00 0.00 0.00 0.86
2501 3846 9.347934 CAGAACTTCATTGACGAGGATATATAC 57.652 37.037 0.00 0.00 0.00 1.47
2502 3847 9.078990 AGAACTTCATTGACGAGGATATATACA 57.921 33.333 0.00 0.00 0.00 2.29
2503 3848 9.347934 GAACTTCATTGACGAGGATATATACAG 57.652 37.037 0.00 0.00 0.00 2.74
2508 3853 9.292195 TCATTGACGAGGATATATACAGTTACA 57.708 33.333 0.00 0.00 0.00 2.41
2650 3996 7.245604 TGAATGTTCGATGAATCAATGTTCAG 58.754 34.615 0.00 0.00 41.05 3.02
2651 3997 5.550232 TGTTCGATGAATCAATGTTCAGG 57.450 39.130 0.00 1.27 41.05 3.86
2661 4007 7.359595 TGAATCAATGTTCAGGTTTTTACGAG 58.640 34.615 0.00 0.00 33.41 4.18
2755 4101 0.398522 ACCGAGGATGGTGATGGCTA 60.399 55.000 0.00 0.00 41.85 3.93
2805 4151 4.632327 TGATGTAATGTGAACCTGGTCA 57.368 40.909 0.00 0.00 0.00 4.02
2941 4287 5.562506 TCAAGTCTCGAGTAACACCTATG 57.437 43.478 13.13 3.49 0.00 2.23
2945 4291 4.580995 AGTCTCGAGTAACACCTATGATGG 59.419 45.833 13.13 0.00 0.00 3.51
3012 4359 3.067106 ACACGGATAGTTTTGCAGACAG 58.933 45.455 5.28 0.00 0.00 3.51
3024 4371 3.106242 TGCAGACAGTAGCTTTTTCGA 57.894 42.857 0.00 0.00 0.00 3.71
3045 4392 5.639506 TCGACTCTGGATTCTGAATTTTGTC 59.360 40.000 4.11 8.12 0.00 3.18
3076 4423 4.688879 TGTTAGAACACATGCGAAAGGTAG 59.311 41.667 0.00 0.00 33.17 3.18
3077 4424 3.678056 AGAACACATGCGAAAGGTAGA 57.322 42.857 0.00 0.00 0.00 2.59
3078 4425 3.326747 AGAACACATGCGAAAGGTAGAC 58.673 45.455 0.00 0.00 0.00 2.59
3079 4426 2.831685 ACACATGCGAAAGGTAGACA 57.168 45.000 0.00 0.00 0.00 3.41
3080 4427 2.688507 ACACATGCGAAAGGTAGACAG 58.311 47.619 0.00 0.00 0.00 3.51
3081 4428 2.299013 ACACATGCGAAAGGTAGACAGA 59.701 45.455 0.00 0.00 0.00 3.41
3083 4430 3.745975 CACATGCGAAAGGTAGACAGAAA 59.254 43.478 0.00 0.00 0.00 2.52
3084 4431 4.393062 CACATGCGAAAGGTAGACAGAAAT 59.607 41.667 0.00 0.00 0.00 2.17
3086 4433 5.812642 ACATGCGAAAGGTAGACAGAAATAG 59.187 40.000 0.00 0.00 0.00 1.73
3087 4434 5.654603 TGCGAAAGGTAGACAGAAATAGA 57.345 39.130 0.00 0.00 0.00 1.98
3088 4435 5.408356 TGCGAAAGGTAGACAGAAATAGAC 58.592 41.667 0.00 0.00 0.00 2.59
3089 4436 5.047590 TGCGAAAGGTAGACAGAAATAGACA 60.048 40.000 0.00 0.00 0.00 3.41
3090 4437 5.288952 GCGAAAGGTAGACAGAAATAGACAC 59.711 44.000 0.00 0.00 0.00 3.67
3091 4438 5.512082 CGAAAGGTAGACAGAAATAGACACG 59.488 44.000 0.00 0.00 0.00 4.49
3147 4494 0.824182 AGAATACTCCCTCCGCTCCG 60.824 60.000 0.00 0.00 0.00 4.63
3158 4505 2.464865 CTCCGCTCCGAAATACTTCTG 58.535 52.381 0.00 0.00 0.00 3.02
3165 4512 4.599047 CTCCGAAATACTTCTGGAGTACG 58.401 47.826 13.26 0.00 43.38 3.67
3166 4513 4.012374 TCCGAAATACTTCTGGAGTACGT 58.988 43.478 0.00 0.00 43.38 3.57
3167 4514 5.185454 TCCGAAATACTTCTGGAGTACGTA 58.815 41.667 0.00 0.00 43.38 3.57
3168 4515 5.065218 TCCGAAATACTTCTGGAGTACGTAC 59.935 44.000 18.10 18.10 43.38 3.67
3219 4566 7.676683 TGAATATATATACTCCTGGCTTCCC 57.323 40.000 0.00 0.00 0.00 3.97
3222 4569 1.119574 TATACTCCTGGCTTCCCGGC 61.120 60.000 0.00 0.00 36.07 6.13
3223 4570 2.898472 ATACTCCTGGCTTCCCGGCT 62.898 60.000 0.00 0.00 39.32 5.52
3244 4609 1.993370 GGTAGCTCGTGTTAACTGCTG 59.007 52.381 18.70 5.87 35.99 4.41
3303 4668 0.324285 AAGGAGCTGCAGAGGAACAG 59.676 55.000 20.43 0.00 36.96 3.16
3306 4671 1.654317 GAGCTGCAGAGGAACAGATG 58.346 55.000 20.43 0.00 35.90 2.90
3427 4792 0.254462 TGCAGAGGACACAACACCAA 59.746 50.000 0.00 0.00 0.00 3.67
3482 4847 4.895668 AAAAATGCCAGTTGATGATGGT 57.104 36.364 0.00 0.00 38.91 3.55
3493 4858 4.284490 AGTTGATGATGGTAGTGTGTCTGT 59.716 41.667 0.00 0.00 0.00 3.41
3546 4911 3.713003 TCTAAGGCTGAGAATGAGACCA 58.287 45.455 0.00 0.00 0.00 4.02
3548 4913 1.202330 AGGCTGAGAATGAGACCAGG 58.798 55.000 0.00 0.00 0.00 4.45
3595 4960 3.959975 GCGAAAACACCCTGCGCA 61.960 61.111 10.98 10.98 46.19 6.09
3707 6525 0.676736 CCTCCTAGATTCCTCGCCAC 59.323 60.000 0.00 0.00 0.00 5.01
3710 6528 1.107538 CCTAGATTCCTCGCCACCGA 61.108 60.000 0.00 0.00 42.01 4.69
3728 6546 1.872773 GACCCTCCACTCTCTTCCAT 58.127 55.000 0.00 0.00 0.00 3.41
3803 6621 3.412237 TGTAGTTAGGCCAACTCCAAC 57.588 47.619 19.64 14.47 44.48 3.77
3822 6640 1.695893 CGCACGACCGCATTTGATCT 61.696 55.000 0.00 0.00 0.00 2.75
3823 6641 0.247814 GCACGACCGCATTTGATCTG 60.248 55.000 0.00 0.00 0.00 2.90
3827 6645 2.002586 CGACCGCATTTGATCTGTCTT 58.997 47.619 0.00 0.00 0.00 3.01
3839 6657 7.408756 TTTGATCTGTCTTTATCCATTTGGG 57.591 36.000 0.00 0.00 35.41 4.12
3842 6660 5.512942 TCTGTCTTTATCCATTTGGGTCA 57.487 39.130 0.00 0.00 38.11 4.02
3847 6665 4.941263 TCTTTATCCATTTGGGTCAGAACG 59.059 41.667 0.00 0.00 38.11 3.95
3861 6679 2.540931 TCAGAACGGACTACAAAAACGC 59.459 45.455 0.00 0.00 0.00 4.84
3866 6684 1.232621 GGACTACAAAAACGCGGCCT 61.233 55.000 12.47 0.00 0.00 5.19
3884 6702 0.518355 CTAATGCACCGACGCAAACG 60.518 55.000 2.77 0.00 46.87 3.60
3909 6727 1.886542 GGCGTCCATTTTCTGTCCTTT 59.113 47.619 0.00 0.00 0.00 3.11
4005 6823 2.365105 TTGTCCTCCCCTAGCCCG 60.365 66.667 0.00 0.00 0.00 6.13
4038 6856 0.485543 AACGTCCCCATTTCCCCTTT 59.514 50.000 0.00 0.00 0.00 3.11
4078 6896 3.402681 CTCCGGCTCCCACCATGT 61.403 66.667 0.00 0.00 0.00 3.21
4084 6902 2.905996 GCTCCCACCATGTCCACCA 61.906 63.158 0.00 0.00 0.00 4.17
4133 6951 2.045926 CGCCCCTTGACCCTGAAG 60.046 66.667 0.00 0.00 0.00 3.02
4142 6960 4.322567 CCTTGACCCTGAAGAAGAAGAAG 58.677 47.826 0.00 0.00 0.00 2.85
4161 6979 2.639286 CCAAGAAGGTGCACACGC 59.361 61.111 20.43 6.57 39.24 5.34
4200 7018 2.543067 AATGACGAAGAGGGCTGGCC 62.543 60.000 13.15 13.15 0.00 5.36
4228 7046 0.326264 AATGCTGCGGAGAGGAAAGT 59.674 50.000 8.65 0.00 0.00 2.66
4265 7083 2.659244 GACGACGTCGGGCAACAA 60.659 61.111 37.89 0.00 44.95 2.83
4266 7084 2.935446 GACGACGTCGGGCAACAAC 61.935 63.158 37.89 16.20 44.95 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.358406 TGAGATTCCAGCATTAATACATGATTT 57.642 29.630 0.00 0.00 0.00 2.17
10 11 8.790718 GTGAGATTCCAGCATTAATACATGATT 58.209 33.333 0.00 0.00 0.00 2.57
53 54 5.437060 TGGGCAGAATAACTTATTCAGGAC 58.563 41.667 19.35 14.05 45.41 3.85
112 113 3.432890 GGATCTGGGGAAGAAGTCATGAC 60.433 52.174 18.47 18.47 38.79 3.06
140 149 8.328014 GGCACTAGGGAGTAGTATTAGTAGTAT 58.672 40.741 0.00 0.00 40.27 2.12
161 170 5.304101 TCATTTACTTTTCAACATGGGCACT 59.696 36.000 0.00 0.00 0.00 4.40
243 283 2.076100 CAAGCAAAGTACCATCTCGCA 58.924 47.619 0.00 0.00 0.00 5.10
260 300 1.493311 GCTTCCTCGCGTTCACAAG 59.507 57.895 5.77 3.95 0.00 3.16
292 1454 9.696917 CTTTTCATATAGCAATACAAATTCCCC 57.303 33.333 0.00 0.00 0.00 4.81
356 1524 7.495901 TCTAAGCAAAAACCATTTCAATCACA 58.504 30.769 0.00 0.00 0.00 3.58
375 1543 0.179124 CGACTCAGCCACCTCTAAGC 60.179 60.000 0.00 0.00 0.00 3.09
387 1555 9.210426 GTATAATGCAAAACAAATACGACTCAG 57.790 33.333 0.00 0.00 0.00 3.35
419 1593 3.072184 ACCCTTCTAATCCATGCAGCTAG 59.928 47.826 0.00 0.00 0.00 3.42
420 1594 3.048600 ACCCTTCTAATCCATGCAGCTA 58.951 45.455 0.00 0.00 0.00 3.32
421 1595 1.849039 ACCCTTCTAATCCATGCAGCT 59.151 47.619 0.00 0.00 0.00 4.24
429 1603 9.847224 TGAAAGAATAATACACCCTTCTAATCC 57.153 33.333 0.00 0.00 0.00 3.01
435 1609 5.501897 CGCGTGAAAGAATAATACACCCTTC 60.502 44.000 0.00 0.00 0.00 3.46
439 1613 3.308866 AGCGCGTGAAAGAATAATACACC 59.691 43.478 8.43 0.00 0.00 4.16
450 1624 1.133253 CATGGACAGCGCGTGAAAG 59.867 57.895 8.43 0.00 0.00 2.62
514 1688 1.474478 TGACGAGCTCTGACTTCATCC 59.526 52.381 12.85 0.00 0.00 3.51
565 1739 2.456119 CGGCGCGCTGAAAAGATCT 61.456 57.895 35.90 0.00 0.00 2.75
633 1807 2.179517 CTGCGTCCGGTCAGAGAC 59.820 66.667 13.29 0.00 32.26 3.36
656 1830 1.269517 GCTATCCTCAACAGAGCGGAG 60.270 57.143 0.00 0.00 0.00 4.63
657 1831 0.747255 GCTATCCTCAACAGAGCGGA 59.253 55.000 0.00 0.00 0.00 5.54
658 1832 3.280920 GCTATCCTCAACAGAGCGG 57.719 57.895 0.00 0.00 0.00 5.52
660 1834 1.537135 GGTCGCTATCCTCAACAGAGC 60.537 57.143 0.00 0.00 0.00 4.09
661 1835 1.751351 TGGTCGCTATCCTCAACAGAG 59.249 52.381 0.00 0.00 0.00 3.35
724 1898 4.829968 CTGCTATCCAGTTCTATCCATGG 58.170 47.826 4.97 4.97 36.79 3.66
745 1919 7.463961 TTTTTACTAGACTGGAAGATCGACT 57.536 36.000 0.00 0.00 37.43 4.18
753 1927 7.177216 TCGGTGACTATTTTTACTAGACTGGAA 59.823 37.037 0.00 0.00 0.00 3.53
754 1928 6.660521 TCGGTGACTATTTTTACTAGACTGGA 59.339 38.462 0.00 0.00 0.00 3.86
755 1929 6.860080 TCGGTGACTATTTTTACTAGACTGG 58.140 40.000 0.00 0.00 0.00 4.00
757 1931 8.362639 TGTTTCGGTGACTATTTTTACTAGACT 58.637 33.333 0.00 0.00 0.00 3.24
758 1932 8.524870 TGTTTCGGTGACTATTTTTACTAGAC 57.475 34.615 0.00 0.00 0.00 2.59
759 1933 9.545105 TTTGTTTCGGTGACTATTTTTACTAGA 57.455 29.630 0.00 0.00 0.00 2.43
761 1935 9.934190 GTTTTGTTTCGGTGACTATTTTTACTA 57.066 29.630 0.00 0.00 0.00 1.82
804 1978 1.226945 GCAACGCTTTTGTGTGCCT 60.227 52.632 0.00 0.00 43.14 4.75
805 1979 1.226945 AGCAACGCTTTTGTGTGCC 60.227 52.632 0.00 0.00 43.14 5.01
816 1990 1.070643 GTGCATTTTGGAAAGCAACGC 60.071 47.619 0.00 0.00 40.68 4.84
817 1991 1.526464 GGTGCATTTTGGAAAGCAACG 59.474 47.619 0.00 0.00 40.68 4.10
832 2010 2.242047 TGTTTAAGTACGCTGGTGCA 57.758 45.000 0.00 0.00 39.64 4.57
841 2019 4.259356 GGGGACACCAGATGTTTAAGTAC 58.741 47.826 0.00 0.00 43.56 2.73
843 2021 2.041216 GGGGGACACCAGATGTTTAAGT 59.959 50.000 0.00 0.00 43.56 2.24
855 2033 1.205460 TTTAGCTCCAGGGGGACACC 61.205 60.000 0.00 0.00 38.64 4.16
971 2156 2.280592 ACGTCGCACCTTTGTCCC 60.281 61.111 0.00 0.00 0.00 4.46
1051 2242 1.136695 TCCCAGCACAAACAAGCAAAG 59.863 47.619 0.00 0.00 0.00 2.77
1103 2298 1.805945 GACACCACCATCTCGCGTC 60.806 63.158 5.77 0.00 0.00 5.19
1140 2335 0.837272 CCGGATGGTTCCATGGTACT 59.163 55.000 19.60 2.32 42.74 2.73
1206 2412 4.329545 GCGTGGGCAGGTGGAAGA 62.330 66.667 0.00 0.00 39.62 2.87
1262 2471 0.729140 CGCTTTTCCACGTGGCATTC 60.729 55.000 30.25 15.29 34.44 2.67
1263 2472 1.285641 CGCTTTTCCACGTGGCATT 59.714 52.632 30.25 0.00 34.44 3.56
1264 2473 2.625823 CCGCTTTTCCACGTGGCAT 61.626 57.895 30.25 0.00 34.44 4.40
1265 2474 3.283684 CCGCTTTTCCACGTGGCA 61.284 61.111 30.25 17.74 34.44 4.92
1329 2541 2.970974 GCCTGCTTCCGTGCTGTTC 61.971 63.158 0.00 0.00 0.00 3.18
1330 2542 2.980233 GCCTGCTTCCGTGCTGTT 60.980 61.111 0.00 0.00 0.00 3.16
1331 2543 4.254709 TGCCTGCTTCCGTGCTGT 62.255 61.111 0.00 0.00 0.00 4.40
1333 2545 4.711949 CCTGCCTGCTTCCGTGCT 62.712 66.667 0.00 0.00 0.00 4.40
1338 2550 4.087892 TCTCGCCTGCCTGCTTCC 62.088 66.667 0.00 0.00 0.00 3.46
1339 2551 2.511145 CTCTCGCCTGCCTGCTTC 60.511 66.667 0.00 0.00 0.00 3.86
1350 2562 2.645730 ATATCTCGAATGGCTCTCGC 57.354 50.000 4.25 0.00 36.25 5.03
1351 2563 5.226396 AGAAAATATCTCGAATGGCTCTCG 58.774 41.667 2.90 2.90 30.46 4.04
1352 2564 6.704512 GAGAAAATATCTCGAATGGCTCTC 57.295 41.667 0.00 0.00 44.89 3.20
1368 2580 7.580910 AGAGAGAGAGAGAGAGATGAGAAAAT 58.419 38.462 0.00 0.00 0.00 1.82
1376 2588 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
1383 2606 3.724478 ACCAGAGAGAGAGAGAGAGAGA 58.276 50.000 0.00 0.00 0.00 3.10
1412 2635 2.847234 TCCTTCCCAGCACCGTGT 60.847 61.111 0.00 0.00 0.00 4.49
1413 2636 2.046892 CTCCTTCCCAGCACCGTG 60.047 66.667 0.00 0.00 0.00 4.94
1414 2637 2.203788 TCTCCTTCCCAGCACCGT 60.204 61.111 0.00 0.00 0.00 4.83
1481 2705 0.971386 AGAGAACGCTTACCGGGAAA 59.029 50.000 6.32 0.00 42.52 3.13
1544 2768 3.490439 TGATTCAGAGCCTCACAACAA 57.510 42.857 0.00 0.00 0.00 2.83
1546 2770 3.603532 TCATGATTCAGAGCCTCACAAC 58.396 45.455 0.00 0.00 0.00 3.32
1964 3194 0.615331 CTGCAGTGCTAGAAGGGGAA 59.385 55.000 17.60 0.00 0.00 3.97
1989 3219 1.342374 GGGGGCATCTTTGAGGAACAT 60.342 52.381 0.00 0.00 0.00 2.71
2006 3236 7.058525 AGGTCTTATATTTAAAAACGGAGGGG 58.941 38.462 0.00 0.00 0.00 4.79
2086 3316 5.452777 GGAGCAAAAAGAGTGAATGTACAC 58.547 41.667 0.00 0.00 40.60 2.90
2087 3317 4.213270 CGGAGCAAAAAGAGTGAATGTACA 59.787 41.667 0.00 0.00 0.00 2.90
2090 3320 3.214328 ACGGAGCAAAAAGAGTGAATGT 58.786 40.909 0.00 0.00 0.00 2.71
2091 3321 3.904136 ACGGAGCAAAAAGAGTGAATG 57.096 42.857 0.00 0.00 0.00 2.67
2094 3324 5.142061 TGTATACGGAGCAAAAAGAGTGA 57.858 39.130 0.00 0.00 0.00 3.41
2095 3325 4.929808 ACTGTATACGGAGCAAAAAGAGTG 59.070 41.667 18.72 0.00 0.00 3.51
2096 3326 5.047235 AGACTGTATACGGAGCAAAAAGAGT 60.047 40.000 18.72 1.37 0.00 3.24
2098 3328 5.168569 CAGACTGTATACGGAGCAAAAAGA 58.831 41.667 18.72 0.00 0.00 2.52
2099 3329 4.929808 ACAGACTGTATACGGAGCAAAAAG 59.070 41.667 18.72 0.00 0.00 2.27
2100 3330 4.890088 ACAGACTGTATACGGAGCAAAAA 58.110 39.130 18.72 0.00 0.00 1.94
2101 3331 4.530710 ACAGACTGTATACGGAGCAAAA 57.469 40.909 18.72 0.00 0.00 2.44
2102 3332 5.847111 ATACAGACTGTATACGGAGCAAA 57.153 39.130 23.71 0.00 41.41 3.68
2103 3333 5.358725 TCAATACAGACTGTATACGGAGCAA 59.641 40.000 24.89 0.00 42.29 3.91
2104 3334 4.885325 TCAATACAGACTGTATACGGAGCA 59.115 41.667 24.89 0.11 42.29 4.26
2105 3335 5.434352 TCAATACAGACTGTATACGGAGC 57.566 43.478 24.89 9.54 42.29 4.70
2106 3336 8.873215 ATTTTCAATACAGACTGTATACGGAG 57.127 34.615 24.89 14.08 42.29 4.63
2107 3337 8.692710 AGATTTTCAATACAGACTGTATACGGA 58.307 33.333 24.89 19.41 42.29 4.69
2108 3338 8.873215 AGATTTTCAATACAGACTGTATACGG 57.127 34.615 24.89 17.81 42.29 4.02
2109 3339 9.737427 AGAGATTTTCAATACAGACTGTATACG 57.263 33.333 24.89 19.17 42.29 3.06
2170 3401 5.049680 ACAAACATAAGTTGAACTAGCACCG 60.050 40.000 0.00 0.00 38.17 4.94
2209 3440 3.863142 AAACTAGTCGGTGCTACGAAT 57.137 42.857 0.00 8.42 45.38 3.34
2307 3548 1.592543 CGAATGCGCTGCTACATACAA 59.407 47.619 9.73 0.00 0.00 2.41
2309 3550 0.508641 CCGAATGCGCTGCTACATAC 59.491 55.000 9.73 0.00 35.83 2.39
2310 3551 0.599991 CCCGAATGCGCTGCTACATA 60.600 55.000 9.73 0.00 35.83 2.29
2313 3554 2.996168 ATCCCCGAATGCGCTGCTAC 62.996 60.000 9.73 0.00 35.83 3.58
2314 3555 2.807107 ATCCCCGAATGCGCTGCTA 61.807 57.895 9.73 0.00 35.83 3.49
2315 3556 4.181010 ATCCCCGAATGCGCTGCT 62.181 61.111 9.73 0.00 35.83 4.24
2317 3558 2.203056 TCATCCCCGAATGCGCTG 60.203 61.111 9.73 0.00 35.83 5.18
2319 3560 2.513666 TGTCATCCCCGAATGCGC 60.514 61.111 0.00 0.00 35.83 6.09
2320 3561 2.180204 GGTGTCATCCCCGAATGCG 61.180 63.158 0.00 0.00 37.24 4.73
2321 3562 1.077787 TGGTGTCATCCCCGAATGC 60.078 57.895 0.00 0.00 0.00 3.56
2323 3564 1.762957 CTAGTGGTGTCATCCCCGAAT 59.237 52.381 0.00 0.00 0.00 3.34
2447 3792 2.892852 CCCCTCTGAAGAAATGCACAAA 59.107 45.455 0.00 0.00 0.00 2.83
2486 3831 8.913487 TCTTGTAACTGTATATATCCTCGTCA 57.087 34.615 0.00 0.00 0.00 4.35
2497 3842 8.645814 TCTCCAGTTTCTCTTGTAACTGTATA 57.354 34.615 12.38 0.26 44.65 1.47
2498 3843 7.540474 TCTCCAGTTTCTCTTGTAACTGTAT 57.460 36.000 12.38 0.00 44.65 2.29
2499 3844 6.971726 TCTCCAGTTTCTCTTGTAACTGTA 57.028 37.500 12.38 0.00 44.65 2.74
2500 3845 5.871396 TCTCCAGTTTCTCTTGTAACTGT 57.129 39.130 12.38 0.00 44.65 3.55
2501 3846 6.931281 TGATTCTCCAGTTTCTCTTGTAACTG 59.069 38.462 7.76 7.76 45.26 3.16
2502 3847 7.067496 TGATTCTCCAGTTTCTCTTGTAACT 57.933 36.000 0.00 0.00 34.78 2.24
2503 3848 7.657761 TCTTGATTCTCCAGTTTCTCTTGTAAC 59.342 37.037 0.00 0.00 0.00 2.50
2508 3853 6.678568 TCTCTTGATTCTCCAGTTTCTCTT 57.321 37.500 0.00 0.00 0.00 2.85
2628 3974 5.649395 ACCTGAACATTGATTCATCGAACAT 59.351 36.000 0.00 0.00 37.93 2.71
2637 3983 7.360361 ACTCGTAAAAACCTGAACATTGATTC 58.640 34.615 0.00 0.00 0.00 2.52
2745 4091 0.179000 CCAGTGAGGTAGCCATCACC 59.821 60.000 9.87 0.00 45.61 4.02
2859 4205 2.252072 TAGGCAACATCAGTCGGGCC 62.252 60.000 0.00 0.00 38.75 5.80
2941 4287 3.944087 AGTTACAAGCTTGGACTCCATC 58.056 45.455 29.18 10.89 31.53 3.51
2945 4291 4.381411 ACTCAAGTTACAAGCTTGGACTC 58.619 43.478 29.18 16.62 42.44 3.36
3012 4359 5.062809 CAGAATCCAGAGTCGAAAAAGCTAC 59.937 44.000 0.00 0.00 0.00 3.58
3024 4371 5.551233 TCGACAAAATTCAGAATCCAGAGT 58.449 37.500 0.00 0.00 0.00 3.24
3069 4416 5.479375 TCCGTGTCTATTTCTGTCTACCTTT 59.521 40.000 0.00 0.00 0.00 3.11
3076 4423 3.512680 CACCTCCGTGTCTATTTCTGTC 58.487 50.000 0.00 0.00 35.10 3.51
3077 4424 3.594603 CACCTCCGTGTCTATTTCTGT 57.405 47.619 0.00 0.00 35.10 3.41
3088 4435 3.926616 AGAAAATAGTCACACCTCCGTG 58.073 45.455 0.00 0.00 46.11 4.94
3089 4436 5.934402 ATAGAAAATAGTCACACCTCCGT 57.066 39.130 0.00 0.00 0.00 4.69
3090 4437 8.888579 AAATATAGAAAATAGTCACACCTCCG 57.111 34.615 0.00 0.00 0.00 4.63
3147 4494 6.198591 GCATGTACGTACTCCAGAAGTATTTC 59.801 42.308 25.12 0.00 42.38 2.17
3158 4505 5.579511 ACAATTGTAAGCATGTACGTACTCC 59.420 40.000 25.12 13.52 0.00 3.85
3165 4512 6.915349 TGGGTTTACAATTGTAAGCATGTAC 58.085 36.000 32.70 24.29 41.53 2.90
3166 4513 7.526142 TTGGGTTTACAATTGTAAGCATGTA 57.474 32.000 32.70 19.31 41.53 2.29
3167 4514 6.412362 TTGGGTTTACAATTGTAAGCATGT 57.588 33.333 32.70 7.44 41.53 3.21
3168 4515 6.534793 GGATTGGGTTTACAATTGTAAGCATG 59.465 38.462 32.70 1.79 41.53 4.06
3219 4566 0.108992 TTAACACGAGCTACCAGCCG 60.109 55.000 0.00 7.27 43.77 5.52
3222 4569 1.993370 GCAGTTAACACGAGCTACCAG 59.007 52.381 8.61 0.00 0.00 4.00
3223 4570 1.616865 AGCAGTTAACACGAGCTACCA 59.383 47.619 8.61 0.00 37.38 3.25
3244 4609 6.437928 TGATGTTACAAAGTGCAGTGATTTC 58.562 36.000 0.00 0.00 0.00 2.17
3303 4668 0.731417 ATTCTGCGCTGCTTCACATC 59.269 50.000 9.73 0.00 0.00 3.06
3306 4671 2.900122 TTTATTCTGCGCTGCTTCAC 57.100 45.000 9.73 0.00 0.00 3.18
3398 4763 3.002791 GTGTCCTCTGCATCGATTTTGA 58.997 45.455 0.00 0.00 0.00 2.69
3482 4847 5.728637 ATGACATGAAGACAGACACACTA 57.271 39.130 0.00 0.00 0.00 2.74
3493 4858 2.483877 GACGGTGCAAATGACATGAAGA 59.516 45.455 0.00 0.00 0.00 2.87
3595 4960 4.265073 CCTTCTCCAAAATTCTGTCCGAT 58.735 43.478 0.00 0.00 0.00 4.18
3707 6525 1.324005 GGAAGAGAGTGGAGGGTCGG 61.324 65.000 0.00 0.00 0.00 4.79
3710 6528 1.577736 CATGGAAGAGAGTGGAGGGT 58.422 55.000 0.00 0.00 0.00 4.34
3728 6546 2.162338 CTAAACTCCGGCGGTCACCA 62.162 60.000 27.32 4.71 0.00 4.17
3803 6621 1.296867 GATCAAATGCGGTCGTGCG 60.297 57.895 0.00 0.00 37.81 5.34
3822 6640 5.512942 TCTGACCCAAATGGATAAAGACA 57.487 39.130 0.00 0.00 37.39 3.41
3823 6641 5.163754 CGTTCTGACCCAAATGGATAAAGAC 60.164 44.000 0.00 0.00 37.39 3.01
3827 6645 3.264706 TCCGTTCTGACCCAAATGGATAA 59.735 43.478 0.00 0.00 36.00 1.75
3839 6657 3.603173 GCGTTTTTGTAGTCCGTTCTGAC 60.603 47.826 0.00 0.00 35.43 3.51
3842 6660 1.523934 CGCGTTTTTGTAGTCCGTTCT 59.476 47.619 0.00 0.00 0.00 3.01
3847 6665 1.208358 GGCCGCGTTTTTGTAGTCC 59.792 57.895 4.92 0.00 0.00 3.85
3861 6679 3.261951 CGTCGGTGCATTAGGCCG 61.262 66.667 6.36 6.36 46.12 6.13
3866 6684 1.493750 CGTTTGCGTCGGTGCATTA 59.506 52.632 3.38 0.00 45.78 1.90
3878 6696 3.810896 GGACGCCCATCCGTTTGC 61.811 66.667 0.00 0.00 42.24 3.68
3909 6727 1.559219 TGGGCTGAAAATGGATCTCGA 59.441 47.619 0.00 0.00 0.00 4.04
3985 6803 2.073101 GGCTAGGGGAGGACAAGGG 61.073 68.421 0.00 0.00 0.00 3.95
4009 6827 2.660802 GGGACGTTGTGACCCGAT 59.339 61.111 0.00 0.00 42.76 4.18
4038 6856 2.555227 GCATGAGGGTTTTGGGAAGAGA 60.555 50.000 0.00 0.00 0.00 3.10
4072 6890 0.260230 TTTGGTGTGGTGGACATGGT 59.740 50.000 0.00 0.00 36.78 3.55
4078 6896 1.391157 GCTTGCTTTGGTGTGGTGGA 61.391 55.000 0.00 0.00 0.00 4.02
4084 6902 3.605664 GGCGGCTTGCTTTGGTGT 61.606 61.111 0.00 0.00 45.43 4.16
4133 6951 2.816672 CACCTTCTTGGGCTTCTTCTTC 59.183 50.000 0.00 0.00 41.11 2.87
4142 6960 2.908073 CGTGTGCACCTTCTTGGGC 61.908 63.158 15.69 0.00 41.11 5.36
4161 6979 3.997064 CTCGGGTGAGCTGCTTCGG 62.997 68.421 2.53 2.04 34.96 4.30
4200 7018 2.173669 CCGCAGCATTGGTCCTACG 61.174 63.158 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.