Multiple sequence alignment - TraesCS6A01G333300

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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 TraesCS6A01G333300 chr6A 100.000 4641 0 0 1 4641 564402117 564406757 0.000000e+00 8571.0
1 TraesCS6A01G333300 chr6A 87.723 1010 95 17 2599 3603 564509412 564510397 0.000000e+00 1151.0
2 TraesCS6A01G333300 chr6A 85.906 596 68 8 927 1521 564507702 564508282 5.100000e-174 621.0
3 TraesCS6A01G333300 chr6A 80.349 687 97 24 2729 3404 564586278 564586937 1.940000e-133 486.0
4 TraesCS6A01G333300 chr6A 83.969 262 37 4 1261 1518 564584668 564584928 3.590000e-61 246.0
5 TraesCS6A01G333300 chr6A 87.162 148 19 0 2219 2366 564509118 564509265 7.990000e-38 169.0
6 TraesCS6A01G333300 chr6B 89.775 2621 178 45 2061 4641 634641144 634643714 0.000000e+00 3273.0
7 TraesCS6A01G333300 chr6B 89.785 1116 66 22 604 1685 634639194 634640295 0.000000e+00 1386.0
8 TraesCS6A01G333300 chr6B 83.099 1349 157 47 2109 3437 634941180 634942477 0.000000e+00 1162.0
9 TraesCS6A01G333300 chr6B 80.870 690 101 22 2729 3404 634978753 634979425 8.900000e-142 514.0
10 TraesCS6A01G333300 chr6B 93.407 273 18 0 1249 1521 634940042 634940314 5.590000e-109 405.0
11 TraesCS6A01G333300 chr6B 90.096 313 19 6 3 308 634638669 634638976 3.370000e-106 396.0
12 TraesCS6A01G333300 chr6B 95.763 236 9 1 328 563 634638965 634639199 3.390000e-101 379.0
13 TraesCS6A01G333300 chr6B 86.245 269 29 7 1256 1518 634976863 634977129 7.600000e-73 285.0
14 TraesCS6A01G333300 chr6B 86.765 204 14 5 1753 1954 634640846 634641038 1.010000e-51 215.0
15 TraesCS6A01G333300 chr6D 88.962 1667 116 35 1938 3570 421474136 421472504 0.000000e+00 1997.0
16 TraesCS6A01G333300 chr6D 90.476 1386 75 21 606 1954 421475453 421474088 0.000000e+00 1775.0
17 TraesCS6A01G333300 chr6D 87.748 808 80 8 2599 3406 421789789 421790577 0.000000e+00 926.0
18 TraesCS6A01G333300 chr6D 81.674 693 97 23 2729 3404 421800355 421801034 2.440000e-152 549.0
19 TraesCS6A01G333300 chr6D 87.028 424 40 8 1095 1518 421788325 421788733 9.100000e-127 464.0
20 TraesCS6A01G333300 chr6D 93.671 237 13 2 328 563 421475685 421475450 2.050000e-93 353.0
21 TraesCS6A01G333300 chr6D 90.566 212 20 0 2159 2370 421789475 421789686 9.830000e-72 281.0
22 TraesCS6A01G333300 chr6D 91.919 198 8 5 1 191 421475948 421475752 2.130000e-68 270.0
23 TraesCS6A01G333300 chr3B 87.000 100 11 2 4538 4636 788085397 788085299 1.370000e-20 111.0
24 TraesCS6A01G333300 chr3B 92.308 52 3 1 3645 3695 345881 345932 6.440000e-09 73.1
25 TraesCS6A01G333300 chr7D 78.621 145 29 2 4032 4175 229835544 229835687 1.370000e-15 95.3
26 TraesCS6A01G333300 chr4A 81.905 105 11 6 3878 3980 4478781 4478683 1.070000e-11 82.4
27 TraesCS6A01G333300 chr4A 79.661 118 16 6 3865 3980 4248019 4247908 1.380000e-10 78.7
28 TraesCS6A01G333300 chr2B 100.000 38 0 0 2328 2365 109880266 109880303 2.320000e-08 71.3
29 TraesCS6A01G333300 chr1D 81.013 79 14 1 3865 3942 447242532 447242610 1.390000e-05 62.1
30 TraesCS6A01G333300 chr1A 76.786 112 24 2 4023 4133 20972939 20973049 1.390000e-05 62.1
31 TraesCS6A01G333300 chr5A 89.796 49 2 3 3648 3694 40616283 40616236 5.010000e-05 60.2
32 TraesCS6A01G333300 chr4B 88.636 44 3 2 3648 3690 157667268 157667310 8.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G333300 chr6A 564402117 564406757 4640 False 8571.00 8571 100.000000 1 4641 1 chr6A.!!$F1 4640
1 TraesCS6A01G333300 chr6A 564507702 564510397 2695 False 647.00 1151 86.930333 927 3603 3 chr6A.!!$F2 2676
2 TraesCS6A01G333300 chr6A 564584668 564586937 2269 False 366.00 486 82.159000 1261 3404 2 chr6A.!!$F3 2143
3 TraesCS6A01G333300 chr6B 634638669 634643714 5045 False 1129.80 3273 90.436800 3 4641 5 chr6B.!!$F1 4638
4 TraesCS6A01G333300 chr6B 634940042 634942477 2435 False 783.50 1162 88.253000 1249 3437 2 chr6B.!!$F2 2188
5 TraesCS6A01G333300 chr6B 634976863 634979425 2562 False 399.50 514 83.557500 1256 3404 2 chr6B.!!$F3 2148
6 TraesCS6A01G333300 chr6D 421472504 421475948 3444 True 1098.75 1997 91.257000 1 3570 4 chr6D.!!$R1 3569
7 TraesCS6A01G333300 chr6D 421788325 421790577 2252 False 557.00 926 88.447333 1095 3406 3 chr6D.!!$F2 2311
8 TraesCS6A01G333300 chr6D 421800355 421801034 679 False 549.00 549 81.674000 2729 3404 1 chr6D.!!$F1 675

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
815 830 1.211743 GCCAAAGCAAGCTTGTTCAC 58.788 50.0 26.55 10.74 39.53 3.18 F
2376 4021 0.109086 ATCAAGGTCAGTCTCGCACG 60.109 55.0 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 4082 0.165944 GCAGTGCACGCGATTAGTTT 59.834 50.0 15.93 0.0 0.0 2.66 R
4287 6166 0.187606 GGGTTTGTCAGAAAGGGGGT 59.812 55.0 0.00 0.0 0.0 4.95 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
80 88 1.956477 AGTGAAAACTCCCACATGTGC 59.044 47.619 20.81 4.65 35.84 4.57
213 224 5.989551 ATTTGCACTTTGTTTCCACATTC 57.010 34.783 0.00 0.00 31.06 2.67
214 225 4.734398 TTGCACTTTGTTTCCACATTCT 57.266 36.364 0.00 0.00 31.06 2.40
220 231 6.491394 CACTTTGTTTCCACATTCTTTCGTA 58.509 36.000 0.00 0.00 31.06 3.43
228 239 5.812652 TCCACATTCTTTCGTAAACACAAC 58.187 37.500 0.00 0.00 0.00 3.32
267 278 6.959361 ACATTTTGATCCTTGTACGCATATC 58.041 36.000 0.00 0.00 0.00 1.63
296 308 2.813908 GCGCGGGTAGACACCTTG 60.814 66.667 8.83 0.00 45.04 3.61
297 309 2.654877 CGCGGGTAGACACCTTGT 59.345 61.111 0.00 0.00 45.04 3.16
309 321 4.547406 GACACCTTGTCAACCACTAAAC 57.453 45.455 1.34 0.00 46.22 2.01
310 322 4.196971 GACACCTTGTCAACCACTAAACT 58.803 43.478 1.34 0.00 46.22 2.66
311 323 4.595986 ACACCTTGTCAACCACTAAACTT 58.404 39.130 0.00 0.00 0.00 2.66
312 324 5.014202 ACACCTTGTCAACCACTAAACTTT 58.986 37.500 0.00 0.00 0.00 2.66
313 325 5.479027 ACACCTTGTCAACCACTAAACTTTT 59.521 36.000 0.00 0.00 0.00 2.27
314 326 6.014925 ACACCTTGTCAACCACTAAACTTTTT 60.015 34.615 0.00 0.00 0.00 1.94
397 409 3.649986 GGTGAGCGCACGCAAACT 61.650 61.111 19.76 0.00 46.09 2.66
434 446 1.689273 GATGAGACCAGATAACCGCCT 59.311 52.381 0.00 0.00 0.00 5.52
459 471 5.128171 TCCTTTATACACGTACATGCTTCCT 59.872 40.000 0.00 0.00 0.00 3.36
563 575 2.547826 GCCCCTTCAACATCTACGTAC 58.452 52.381 0.00 0.00 0.00 3.67
564 576 2.805845 CCCCTTCAACATCTACGTACG 58.194 52.381 15.01 15.01 0.00 3.67
565 577 2.165030 CCCCTTCAACATCTACGTACGT 59.835 50.000 25.98 25.98 0.00 3.57
566 578 3.378112 CCCCTTCAACATCTACGTACGTA 59.622 47.826 25.41 25.41 0.00 3.57
567 579 4.142403 CCCCTTCAACATCTACGTACGTAA 60.142 45.833 26.68 18.09 0.00 3.18
568 580 5.450965 CCCCTTCAACATCTACGTACGTAAT 60.451 44.000 26.68 19.30 0.00 1.89
569 581 6.038356 CCCTTCAACATCTACGTACGTAATT 58.962 40.000 26.68 15.21 0.00 1.40
570 582 6.532657 CCCTTCAACATCTACGTACGTAATTT 59.467 38.462 26.68 14.84 0.00 1.82
571 583 7.253883 CCCTTCAACATCTACGTACGTAATTTC 60.254 40.741 26.68 0.00 0.00 2.17
572 584 7.487189 CCTTCAACATCTACGTACGTAATTTCT 59.513 37.037 26.68 10.62 0.00 2.52
573 585 8.746922 TTCAACATCTACGTACGTAATTTCTT 57.253 30.769 26.68 12.71 0.00 2.52
574 586 8.746922 TCAACATCTACGTACGTAATTTCTTT 57.253 30.769 26.68 13.31 0.00 2.52
575 587 9.195411 TCAACATCTACGTACGTAATTTCTTTT 57.805 29.630 26.68 11.96 0.00 2.27
576 588 9.801714 CAACATCTACGTACGTAATTTCTTTTT 57.198 29.630 26.68 10.59 0.00 1.94
648 660 4.868314 TCTCATGCACATCCTGATCTAG 57.132 45.455 0.00 0.00 0.00 2.43
668 680 7.307131 TCTAGACAATTATCTCATGCCATGA 57.693 36.000 7.26 7.26 37.76 3.07
755 770 6.501781 GCAATTATCTCATGCCATATAAGCC 58.498 40.000 0.00 0.00 34.03 4.35
815 830 1.211743 GCCAAAGCAAGCTTGTTCAC 58.788 50.000 26.55 10.74 39.53 3.18
1005 1025 0.742281 GCACTCGTCTCCATGCACAT 60.742 55.000 0.00 0.00 38.00 3.21
1006 1026 1.004595 CACTCGTCTCCATGCACATG 58.995 55.000 3.56 3.56 38.51 3.21
1010 1030 3.323115 ACTCGTCTCCATGCACATGATAT 59.677 43.478 12.18 0.00 41.20 1.63
1050 1071 1.206878 TGCACCCTACAGCTGATCAT 58.793 50.000 23.35 0.00 0.00 2.45
1053 1074 2.547642 GCACCCTACAGCTGATCATCTC 60.548 54.545 23.35 0.48 0.00 2.75
1058 1079 1.189752 ACAGCTGATCATCTCCACGT 58.810 50.000 23.35 0.00 0.00 4.49
1067 1088 0.385751 CATCTCCACGTCGTAGCCAT 59.614 55.000 0.00 0.00 0.00 4.40
1079 1100 1.795286 CGTAGCCATAGCAGCTTTAGC 59.205 52.381 0.00 0.00 43.56 3.09
1096 1131 6.478588 GCTTTAGCTTCACATACATACACAC 58.521 40.000 0.00 0.00 38.21 3.82
1400 1438 4.626081 AAGGTGCTCGCCACGCTT 62.626 61.111 2.02 3.25 45.62 4.68
1414 1452 4.329545 GCTTGACCAGGCGTCCCA 62.330 66.667 0.00 0.00 41.18 4.37
1416 1454 4.308458 TTGACCAGGCGTCCCACG 62.308 66.667 0.00 0.00 45.88 4.94
1538 1579 3.482722 CGTTGAACGGAGAAGCTACTA 57.517 47.619 10.31 0.00 38.08 1.82
1541 1582 3.083122 TGAACGGAGAAGCTACTAGGT 57.917 47.619 0.00 0.00 0.00 3.08
1595 1664 3.620427 TTGCGGGTAATCTTTAGAGCA 57.380 42.857 0.00 0.00 0.00 4.26
1599 1668 4.344102 TGCGGGTAATCTTTAGAGCATACT 59.656 41.667 0.00 0.00 0.00 2.12
1613 1682 4.340950 AGAGCATACTCCAAAGAGAGCTAC 59.659 45.833 0.00 0.00 44.65 3.58
1645 1714 6.879276 TGAATTTTATGGGTTTGTCGTACA 57.121 33.333 0.00 0.00 0.00 2.90
1750 2219 7.867403 AGCTAATAACCACATGTTGTCAAAAAG 59.133 33.333 2.61 0.16 37.83 2.27
1941 3296 2.840102 TTTTTGTGCGGGGTGGGG 60.840 61.111 0.00 0.00 0.00 4.96
1943 3298 2.294170 TTTTTGTGCGGGGTGGGGTA 62.294 55.000 0.00 0.00 0.00 3.69
1944 3299 2.294170 TTTTGTGCGGGGTGGGGTAA 62.294 55.000 0.00 0.00 0.00 2.85
1945 3300 2.980105 TTTGTGCGGGGTGGGGTAAC 62.980 60.000 0.00 0.00 0.00 2.50
1948 3303 2.360726 GCGGGGTGGGGTAACAAG 60.361 66.667 0.00 0.00 39.74 3.16
1949 3304 3.163503 CGGGGTGGGGTAACAAGT 58.836 61.111 0.00 0.00 39.74 3.16
1950 3305 1.457165 CGGGGTGGGGTAACAAGTT 59.543 57.895 0.00 0.00 39.74 2.66
1952 3307 1.624336 GGGGTGGGGTAACAAGTTTC 58.376 55.000 0.00 0.00 39.74 2.78
1953 3308 1.624336 GGGTGGGGTAACAAGTTTCC 58.376 55.000 0.46 0.46 39.74 3.13
1954 3309 1.624336 GGTGGGGTAACAAGTTTCCC 58.376 55.000 16.68 16.68 45.99 3.97
1955 3310 1.146359 GGTGGGGTAACAAGTTTCCCT 59.854 52.381 21.97 0.00 45.97 4.20
1956 3311 2.425247 GGTGGGGTAACAAGTTTCCCTT 60.425 50.000 21.97 0.00 45.97 3.95
1958 3313 3.707611 GTGGGGTAACAAGTTTCCCTTTT 59.292 43.478 21.97 0.00 45.97 2.27
1960 3315 4.406326 TGGGGTAACAAGTTTCCCTTTTTC 59.594 41.667 21.97 9.64 45.97 2.29
1962 3317 5.129815 GGGGTAACAAGTTTCCCTTTTTCTT 59.870 40.000 21.97 0.00 45.97 2.52
1964 3319 6.759827 GGGTAACAAGTTTCCCTTTTTCTTTC 59.240 38.462 17.42 0.00 44.10 2.62
1965 3320 6.759827 GGTAACAAGTTTCCCTTTTTCTTTCC 59.240 38.462 0.00 0.00 0.00 3.13
1967 3322 4.142026 ACAAGTTTCCCTTTTTCTTTCCGG 60.142 41.667 0.00 0.00 0.00 5.14
1968 3323 2.963101 AGTTTCCCTTTTTCTTTCCGGG 59.037 45.455 0.00 0.00 36.21 5.73
1969 3324 2.696707 GTTTCCCTTTTTCTTTCCGGGT 59.303 45.455 0.00 0.00 36.30 5.28
1970 3325 3.880168 TTCCCTTTTTCTTTCCGGGTA 57.120 42.857 0.00 0.00 36.30 3.69
2081 3598 7.859377 GCACCAATTCATGATGAACATTACTAG 59.141 37.037 10.45 0.00 39.45 2.57
2230 3816 1.203441 ACTTGATCCTGAGCCTGGCA 61.203 55.000 22.65 0.00 0.00 4.92
2245 3890 0.754957 TGGCAAACAACTGGGGTGAG 60.755 55.000 0.00 0.00 0.00 3.51
2370 4015 2.705658 TGAACCACATCAAGGTCAGTCT 59.294 45.455 0.00 0.00 38.76 3.24
2374 4019 0.969149 ACATCAAGGTCAGTCTCGCA 59.031 50.000 0.00 0.00 0.00 5.10
2375 4020 1.337260 ACATCAAGGTCAGTCTCGCAC 60.337 52.381 0.00 0.00 0.00 5.34
2376 4021 0.109086 ATCAAGGTCAGTCTCGCACG 60.109 55.000 0.00 0.00 0.00 5.34
2377 4022 1.007271 CAAGGTCAGTCTCGCACGT 60.007 57.895 0.00 0.00 0.00 4.49
2378 4023 0.240145 CAAGGTCAGTCTCGCACGTA 59.760 55.000 0.00 0.00 0.00 3.57
2380 4025 0.887836 AGGTCAGTCTCGCACGTACA 60.888 55.000 0.00 0.00 0.00 2.90
2381 4026 0.170561 GGTCAGTCTCGCACGTACAT 59.829 55.000 0.00 0.00 0.00 2.29
2382 4027 1.260206 GTCAGTCTCGCACGTACATG 58.740 55.000 0.00 0.00 0.00 3.21
2384 4029 0.732538 CAGTCTCGCACGTACATGCA 60.733 55.000 15.00 0.47 46.47 3.96
2385 4030 0.732880 AGTCTCGCACGTACATGCAC 60.733 55.000 15.00 4.75 46.47 4.57
2386 4031 1.799916 TCTCGCACGTACATGCACG 60.800 57.895 16.81 16.81 46.47 5.34
2395 4040 1.556564 GTACATGCACGTGTATCGCT 58.443 50.000 16.73 4.85 44.19 4.93
2396 4041 2.723209 GTACATGCACGTGTATCGCTA 58.277 47.619 16.73 3.90 44.19 4.26
2397 4042 2.287393 ACATGCACGTGTATCGCTAA 57.713 45.000 16.73 0.00 44.19 3.09
2416 4069 1.151777 ATTAATCGCGTGCACTCCCG 61.152 55.000 16.19 14.36 0.00 5.14
2428 4081 2.289195 TGCACTCCCGTCGAATAAACTT 60.289 45.455 0.00 0.00 0.00 2.66
2429 4082 3.056678 TGCACTCCCGTCGAATAAACTTA 60.057 43.478 0.00 0.00 0.00 2.24
2430 4083 3.928375 GCACTCCCGTCGAATAAACTTAA 59.072 43.478 0.00 0.00 0.00 1.85
2431 4084 4.389687 GCACTCCCGTCGAATAAACTTAAA 59.610 41.667 0.00 0.00 0.00 1.52
2432 4085 5.669602 GCACTCCCGTCGAATAAACTTAAAC 60.670 44.000 0.00 0.00 0.00 2.01
2433 4086 5.636543 CACTCCCGTCGAATAAACTTAAACT 59.363 40.000 0.00 0.00 0.00 2.66
2454 4107 2.517391 ATCGCGTGCACTGCATGTTG 62.517 55.000 25.50 15.39 46.10 3.33
2477 4130 3.067846 GCCGTCACGTTAAGCTCGC 62.068 63.158 0.00 0.00 0.00 5.03
2478 4131 2.442188 CCGTCACGTTAAGCTCGCC 61.442 63.158 0.00 0.00 0.00 5.54
2499 4169 2.352651 CCATCGTTGGCATCTTGTGTAG 59.647 50.000 0.00 0.00 35.85 2.74
2500 4170 2.831685 TCGTTGGCATCTTGTGTAGT 57.168 45.000 0.00 0.00 0.00 2.73
2501 4171 3.945981 TCGTTGGCATCTTGTGTAGTA 57.054 42.857 0.00 0.00 0.00 1.82
2502 4172 3.581755 TCGTTGGCATCTTGTGTAGTAC 58.418 45.455 0.00 0.00 0.00 2.73
2503 4173 2.344441 CGTTGGCATCTTGTGTAGTACG 59.656 50.000 0.00 0.00 0.00 3.67
2524 4214 0.031585 GCCGAGATGCACCGTATACA 59.968 55.000 3.32 0.00 0.00 2.29
2533 4223 2.689471 TGCACCGTATACACTTCCGTAT 59.311 45.455 3.32 0.00 36.13 3.06
2562 4256 4.801330 TCCTTGGATATGCACCGTATAG 57.199 45.455 0.00 0.00 0.00 1.31
2597 4291 5.149273 GTCGATCGTTAACTCTTGTGTACA 58.851 41.667 15.94 0.00 0.00 2.90
2825 4652 2.050934 GGGTTCTACGGCGACTCCT 61.051 63.158 16.62 0.00 0.00 3.69
2950 4780 2.267961 CCCGACCAGTGGTAAGCC 59.732 66.667 16.72 1.10 35.25 4.35
2961 4791 2.200373 TGGTAAGCCAAAGAGAAGCC 57.800 50.000 0.00 0.00 42.83 4.35
2962 4792 1.423541 TGGTAAGCCAAAGAGAAGCCA 59.576 47.619 0.00 0.00 42.83 4.75
2963 4793 1.813178 GGTAAGCCAAAGAGAAGCCAC 59.187 52.381 0.00 0.00 34.09 5.01
2964 4794 2.504367 GTAAGCCAAAGAGAAGCCACA 58.496 47.619 0.00 0.00 0.00 4.17
2965 4795 1.322442 AAGCCAAAGAGAAGCCACAC 58.678 50.000 0.00 0.00 0.00 3.82
2969 4808 2.575532 CCAAAGAGAAGCCACACAAGA 58.424 47.619 0.00 0.00 0.00 3.02
2979 4818 4.311816 AGCCACACAAGAACATTTTCTG 57.688 40.909 0.00 0.00 41.56 3.02
3020 4870 1.987704 TTTGTGCTGACCGTGTGTGC 61.988 55.000 0.00 0.00 0.00 4.57
3024 4874 2.584970 CTGACCGTGTGTGCGTGT 60.585 61.111 0.00 0.00 0.00 4.49
3025 4875 2.870341 CTGACCGTGTGTGCGTGTG 61.870 63.158 0.00 0.00 0.00 3.82
3026 4876 3.636043 GACCGTGTGTGCGTGTGG 61.636 66.667 0.00 0.00 0.00 4.17
3029 4879 3.572539 CGTGTGTGCGTGTGGCTT 61.573 61.111 0.00 0.00 44.05 4.35
3092 4942 4.082125 GGTGGAGTTCATGAAGAAATGGT 58.918 43.478 8.80 0.00 38.13 3.55
3206 5062 2.484203 GCGACGACTACTTCCGCT 59.516 61.111 0.00 0.00 42.24 5.52
3381 5237 2.202878 GTGCGCTAGGATCGGCAA 60.203 61.111 9.73 0.00 37.12 4.52
3481 5355 1.048601 AGGAAGCAAGGACTCACGAA 58.951 50.000 0.00 0.00 0.00 3.85
3536 5413 4.790140 CGTCAAGATTGCTCACAAATAAGC 59.210 41.667 0.00 0.00 39.77 3.09
3615 5492 8.975410 ACTAATAAAGATTTACCCGCAAAAAC 57.025 30.769 0.00 0.00 0.00 2.43
3627 5504 9.843334 TTTACCCGCAAAAACATACTAATAAAG 57.157 29.630 0.00 0.00 0.00 1.85
3673 5550 6.294564 GGTTTCATCTTTAACTTTCTCCCCAC 60.295 42.308 0.00 0.00 0.00 4.61
3695 5572 1.002502 CCCTTCGTCCAACTTCCCC 60.003 63.158 0.00 0.00 0.00 4.81
3697 5574 1.489560 CCTTCGTCCAACTTCCCCCT 61.490 60.000 0.00 0.00 0.00 4.79
3710 5587 0.404346 TCCCCCTATTTCCCATCCCC 60.404 60.000 0.00 0.00 0.00 4.81
3720 5597 3.655972 TTCCCATCCCCTTCTAGCTAT 57.344 47.619 0.00 0.00 0.00 2.97
3814 5691 8.996651 ATCTTATCTTTGGTAACCCCATAAAG 57.003 34.615 0.00 0.00 44.74 1.85
3868 5745 5.007724 GCCTGTTTAGGGAATGATAGAAACG 59.992 44.000 0.00 0.00 44.75 3.60
3869 5746 6.113411 CCTGTTTAGGGAATGATAGAAACGT 58.887 40.000 0.00 0.00 40.63 3.99
3906 5783 9.195411 TGTCTATTTGTTTTGCATCAAGATTTC 57.805 29.630 0.00 0.00 0.00 2.17
3917 5794 4.816385 GCATCAAGATTTCCTTCGTATGGA 59.184 41.667 0.00 0.00 31.42 3.41
3919 5796 5.414789 TCAAGATTTCCTTCGTATGGACA 57.585 39.130 0.00 0.00 32.65 4.02
3930 5807 6.049149 CCTTCGTATGGACATCTTATTGTGT 58.951 40.000 0.00 0.00 0.00 3.72
4034 5911 9.487790 ACACACTCCAAACATAATAAAAATTGG 57.512 29.630 0.00 0.00 38.88 3.16
4054 5931 4.208746 TGGGGACAAGTATGTTTTTCGTT 58.791 39.130 0.00 0.00 40.74 3.85
4055 5932 4.645588 TGGGGACAAGTATGTTTTTCGTTT 59.354 37.500 0.00 0.00 40.74 3.60
4056 5933 5.217393 GGGGACAAGTATGTTTTTCGTTTC 58.783 41.667 0.00 0.00 40.74 2.78
4064 5941 9.931210 CAAGTATGTTTTTCGTTTCTAAACTCT 57.069 29.630 4.24 0.00 36.77 3.24
4075 5952 8.128016 TCGTTTCTAAACTCTCTTGAAAGTTC 57.872 34.615 4.24 0.00 34.71 3.01
4083 5960 8.620533 AAACTCTCTTGAAAGTTCAAAAATCG 57.379 30.769 7.80 0.00 45.61 3.34
4086 5963 7.281100 ACTCTCTTGAAAGTTCAAAAATCGTCT 59.719 33.333 7.80 0.00 45.61 4.18
4113 5990 5.146010 ACTTCAAAACCAGCAAAACTCAA 57.854 34.783 0.00 0.00 0.00 3.02
4117 5994 4.405358 TCAAAACCAGCAAAACTCAATCCT 59.595 37.500 0.00 0.00 0.00 3.24
4120 5997 3.565307 ACCAGCAAAACTCAATCCTTCA 58.435 40.909 0.00 0.00 0.00 3.02
4125 6002 6.071728 CCAGCAAAACTCAATCCTTCAACTAT 60.072 38.462 0.00 0.00 0.00 2.12
4145 6022 8.883731 CAACTATTGAAACCAGATAATCTTCGT 58.116 33.333 0.00 0.00 0.00 3.85
4157 6034 9.469807 CCAGATAATCTTCGTCCTATATAATGC 57.530 37.037 0.00 0.00 0.00 3.56
4164 6041 8.418597 TCTTCGTCCTATATAATGCTTTAGGT 57.581 34.615 0.00 0.00 34.18 3.08
4168 6045 7.015877 TCGTCCTATATAATGCTTTAGGTGGTT 59.984 37.037 0.00 0.00 34.18 3.67
4180 6059 4.669206 TTAGGTGGTTTGAGTAACGTGA 57.331 40.909 0.00 0.00 37.64 4.35
4189 6068 1.138661 TGAGTAACGTGAACCCGGTTT 59.861 47.619 3.77 0.00 0.00 3.27
4202 6081 6.016860 GTGAACCCGGTTTTTGACTAAATACT 60.017 38.462 3.77 0.00 31.16 2.12
4205 6084 6.772605 ACCCGGTTTTTGACTAAATACTAGT 58.227 36.000 0.00 0.00 31.16 2.57
4206 6085 7.226441 ACCCGGTTTTTGACTAAATACTAGTT 58.774 34.615 0.00 0.00 31.16 2.24
4207 6086 7.173735 ACCCGGTTTTTGACTAAATACTAGTTG 59.826 37.037 0.00 0.00 31.16 3.16
4218 6097 1.578897 TACTAGTTGCATGGCCTGGA 58.421 50.000 3.32 0.00 0.00 3.86
4246 6125 1.758280 ACCACGTCAGTTAAGTGACCA 59.242 47.619 29.23 2.35 43.45 4.02
4261 6140 2.113243 GACCAAAGGACCCTCACGCT 62.113 60.000 0.00 0.00 0.00 5.07
4267 6146 1.115467 AGGACCCTCACGCTTCTATG 58.885 55.000 0.00 0.00 0.00 2.23
4286 6165 2.125106 GTCCCGCACACTCCCATC 60.125 66.667 0.00 0.00 0.00 3.51
4287 6166 2.606213 TCCCGCACACTCCCATCA 60.606 61.111 0.00 0.00 0.00 3.07
4288 6167 2.436646 CCCGCACACTCCCATCAC 60.437 66.667 0.00 0.00 0.00 3.06
4297 6176 0.178831 ACTCCCATCACCCCCTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
4308 6187 1.620822 CCCCTTTCTGACAAACCCTG 58.379 55.000 0.00 0.00 0.00 4.45
4315 6194 4.993705 TTCTGACAAACCCTGAACCTAT 57.006 40.909 0.00 0.00 0.00 2.57
4323 6202 2.240279 ACCCTGAACCTATAGCTAGCG 58.760 52.381 9.55 0.00 0.00 4.26
4325 6204 2.240279 CCTGAACCTATAGCTAGCGGT 58.760 52.381 9.55 7.69 0.00 5.68
4340 6219 2.092291 CGGTGGTGACGGTGATTCG 61.092 63.158 0.00 0.00 0.00 3.34
4352 6231 0.099436 GTGATTCGCTCATGGGTTGC 59.901 55.000 0.00 0.00 35.97 4.17
4380 6259 1.522355 CACTGAGGCATGGCTACGG 60.522 63.158 23.39 20.74 0.00 4.02
4383 6262 2.897350 GAGGCATGGCTACGGCAC 60.897 66.667 23.39 4.57 41.84 5.01
4384 6263 3.391665 GAGGCATGGCTACGGCACT 62.392 63.158 23.39 0.00 41.84 4.40
4400 6279 4.293648 CTGGTGGCGACGTGTCCA 62.294 66.667 0.00 0.00 0.00 4.02
4401 6280 4.293648 TGGTGGCGACGTGTCCAG 62.294 66.667 5.68 0.00 32.15 3.86
4407 6286 3.991051 CGACGTGTCCAGGTGGCT 61.991 66.667 0.00 0.00 34.44 4.75
4469 6348 1.373435 CAACTACGCCCTTCCCACA 59.627 57.895 0.00 0.00 0.00 4.17
4473 6352 0.391263 CTACGCCCTTCCCACAAGTC 60.391 60.000 0.00 0.00 0.00 3.01
4475 6354 1.002134 CGCCCTTCCCACAAGTCAT 60.002 57.895 0.00 0.00 0.00 3.06
4476 6355 0.609131 CGCCCTTCCCACAAGTCATT 60.609 55.000 0.00 0.00 0.00 2.57
4479 6358 3.365472 GCCCTTCCCACAAGTCATTAAT 58.635 45.455 0.00 0.00 0.00 1.40
4481 6360 5.140454 GCCCTTCCCACAAGTCATTAATAT 58.860 41.667 0.00 0.00 0.00 1.28
4502 6381 7.782897 ATATCGACCTTGATTCCAGAGATAA 57.217 36.000 0.00 0.00 0.00 1.75
4559 6438 6.314917 AGGAGTAAGGAAATTCCACACATTT 58.685 36.000 15.21 1.06 39.61 2.32
4581 6460 7.421530 TTTAGTGTTTGTCTCTCTTGTATGC 57.578 36.000 0.00 0.00 0.00 3.14
4604 6483 5.395768 GCATATAGGGTAGTCACATGGATCC 60.396 48.000 4.20 4.20 0.00 3.36
4620 6499 2.040412 GGATCCTGGAGAGGTGTTGTTT 59.960 50.000 3.84 0.00 40.76 2.83
4625 6504 6.049955 TCCTGGAGAGGTGTTGTTTATTAG 57.950 41.667 0.00 0.00 40.76 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 41 9.657121 CACTCTCTTTTCTTTTTGTCTTCATAC 57.343 33.333 0.00 0.00 0.00 2.39
80 88 3.510719 ACAAAATGAAATTCCGCATCCG 58.489 40.909 0.00 0.00 33.67 4.18
175 186 9.783256 AAAGTGCAAATACGGAATCTTAAATAC 57.217 29.630 0.00 0.00 0.00 1.89
181 192 5.705609 ACAAAGTGCAAATACGGAATCTT 57.294 34.783 0.00 0.00 0.00 2.40
213 224 5.728351 TCTTCCTGTTGTGTTTACGAAAG 57.272 39.130 0.00 0.00 0.00 2.62
214 225 6.238538 GGAATCTTCCTGTTGTGTTTACGAAA 60.239 38.462 1.57 0.00 44.11 3.46
220 231 2.293399 GCGGAATCTTCCTGTTGTGTTT 59.707 45.455 7.35 0.00 45.33 2.83
228 239 4.635765 TCAAAATGTAGCGGAATCTTCCTG 59.364 41.667 7.35 2.67 45.33 3.86
243 254 6.767902 AGATATGCGTACAAGGATCAAAATGT 59.232 34.615 0.00 0.00 0.00 2.71
316 328 1.439644 GGGTTGACGCCTGCAAAAA 59.560 52.632 0.00 0.00 0.00 1.94
317 329 2.494530 GGGGTTGACGCCTGCAAAA 61.495 57.895 9.73 0.00 44.66 2.44
318 330 2.909965 GGGGTTGACGCCTGCAAA 60.910 61.111 9.73 0.00 44.66 3.68
325 337 0.461516 GCTAGGTTAGGGGTTGACGC 60.462 60.000 0.00 0.00 0.00 5.19
326 338 0.899720 TGCTAGGTTAGGGGTTGACG 59.100 55.000 0.00 0.00 0.00 4.35
395 407 0.974383 CCTACAAGTCGGGGTTGAGT 59.026 55.000 0.00 0.00 0.00 3.41
396 408 1.263356 TCCTACAAGTCGGGGTTGAG 58.737 55.000 0.00 0.00 0.00 3.02
397 409 1.553248 CATCCTACAAGTCGGGGTTGA 59.447 52.381 0.00 0.00 0.00 3.18
434 446 5.813672 GGAAGCATGTACGTGTATAAAGGAA 59.186 40.000 16.28 0.00 0.00 3.36
546 558 7.487189 AGAAATTACGTACGTAGATGTTGAAGG 59.513 37.037 25.56 0.00 31.71 3.46
601 613 4.902552 ACCAAGATGGGCGTTACGTACG 62.903 54.545 15.01 15.01 46.43 3.67
602 614 1.283736 CCAAGATGGGCGTTACGTAC 58.716 55.000 6.63 0.03 32.67 3.67
603 615 0.896923 ACCAAGATGGGCGTTACGTA 59.103 50.000 6.63 0.00 43.37 3.57
604 616 0.390735 GACCAAGATGGGCGTTACGT 60.391 55.000 6.63 0.00 43.37 3.57
648 660 6.387465 CCATTCATGGCATGAGATAATTGTC 58.613 40.000 27.39 0.00 41.75 3.18
682 694 8.940952 GGCATGAGATAATGGTAAGATTAACTC 58.059 37.037 0.00 0.00 37.83 3.01
689 701 6.825213 GCATATGGCATGAGATAATGGTAAGA 59.175 38.462 10.98 0.00 43.97 2.10
739 751 4.025040 TCCTTGGCTTATATGGCATGAG 57.975 45.455 21.70 14.54 42.07 2.90
752 764 0.543646 ATTGCAGGCTTTCCTTGGCT 60.544 50.000 0.00 0.00 41.93 4.75
755 770 3.604875 AATGATTGCAGGCTTTCCTTG 57.395 42.857 0.00 0.00 41.93 3.61
803 818 3.026630 TCGTCTAGGTGAACAAGCTTG 57.973 47.619 24.84 24.84 37.85 4.01
839 854 2.921797 GCTCTAGGCCGATCGGGTC 61.922 68.421 33.98 18.94 42.41 4.46
840 855 2.913060 GCTCTAGGCCGATCGGGT 60.913 66.667 33.98 4.34 38.44 5.28
1005 1025 3.369546 TCTTCGCTGCGAATGATATCA 57.630 42.857 33.97 12.82 44.85 2.15
1006 1026 7.865875 ATATATCTTCGCTGCGAATGATATC 57.134 36.000 37.29 0.00 44.85 1.63
1010 1030 4.091945 GCAATATATCTTCGCTGCGAATGA 59.908 41.667 33.97 29.61 44.85 2.57
1050 1071 1.306148 CTATGGCTACGACGTGGAGA 58.694 55.000 16.16 0.19 0.00 3.71
1053 1074 0.595053 CTGCTATGGCTACGACGTGG 60.595 60.000 11.56 9.21 39.59 4.94
1058 1079 2.545952 GCTAAAGCTGCTATGGCTACGA 60.546 50.000 0.90 0.00 39.30 3.43
1079 1100 7.826260 TGTATGTGTGTGTATGTATGTGAAG 57.174 36.000 0.00 0.00 0.00 3.02
1083 1104 7.485810 ACGTATGTATGTGTGTGTATGTATGT 58.514 34.615 0.00 0.00 0.00 2.29
1096 1131 3.325870 CCCATGCCTACGTATGTATGTG 58.674 50.000 21.07 11.05 30.66 3.21
1247 1282 1.728672 GACCTTCGCCTCTACTCCG 59.271 63.158 0.00 0.00 0.00 4.63
1536 1577 7.113658 TCCAAAGATTTACTCTAGCACCTAG 57.886 40.000 0.00 0.00 35.57 3.02
1538 1579 6.174049 GTTCCAAAGATTTACTCTAGCACCT 58.826 40.000 0.00 0.00 32.41 4.00
1541 1582 7.624549 AGATGTTCCAAAGATTTACTCTAGCA 58.375 34.615 0.00 0.00 32.41 3.49
1591 1644 3.817709 AGCTCTCTTTGGAGTATGCTC 57.182 47.619 1.56 1.56 40.29 4.26
1592 1645 4.026744 TGTAGCTCTCTTTGGAGTATGCT 58.973 43.478 0.00 0.00 40.87 3.79
1595 1664 4.017808 ACGTGTAGCTCTCTTTGGAGTAT 58.982 43.478 0.00 0.00 40.29 2.12
1599 1668 3.825014 AGTAACGTGTAGCTCTCTTTGGA 59.175 43.478 0.00 0.00 0.00 3.53
1607 1676 7.903431 CCATAAAATTCAAGTAACGTGTAGCTC 59.097 37.037 0.00 0.00 0.00 4.09
1613 1682 7.650104 ACAAACCCATAAAATTCAAGTAACGTG 59.350 33.333 0.00 0.00 0.00 4.49
1880 3229 7.222000 TGGTTGGTATACAATGGAAACTTTC 57.778 36.000 5.01 0.00 41.95 2.62
1939 3294 5.864418 AGAAAAAGGGAAACTTGTTACCC 57.136 39.130 0.00 0.00 36.75 3.69
1941 3296 6.474427 CGGAAAGAAAAAGGGAAACTTGTTAC 59.526 38.462 0.00 0.00 36.75 2.50
1943 3298 5.416083 CGGAAAGAAAAAGGGAAACTTGTT 58.584 37.500 0.00 0.00 39.36 2.83
1944 3299 4.142026 CCGGAAAGAAAAAGGGAAACTTGT 60.142 41.667 0.00 0.00 39.96 3.16
1945 3300 4.368315 CCGGAAAGAAAAAGGGAAACTTG 58.632 43.478 0.00 0.00 39.96 3.16
1948 3303 2.696707 ACCCGGAAAGAAAAAGGGAAAC 59.303 45.455 0.73 0.00 44.70 2.78
1949 3304 3.035055 ACCCGGAAAGAAAAAGGGAAA 57.965 42.857 0.73 0.00 44.70 3.13
1950 3305 2.759839 ACCCGGAAAGAAAAAGGGAA 57.240 45.000 0.73 0.00 44.70 3.97
1952 3307 5.413422 ACCCTACCCGGAAAGAAAAAGGG 62.413 52.174 0.73 9.28 46.55 3.95
1953 3308 2.224942 ACCCTACCCGGAAAGAAAAAGG 60.225 50.000 0.73 0.00 33.16 3.11
1954 3309 3.150458 ACCCTACCCGGAAAGAAAAAG 57.850 47.619 0.73 0.00 33.16 2.27
1955 3310 4.141298 TGTTACCCTACCCGGAAAGAAAAA 60.141 41.667 0.73 0.00 33.16 1.94
1956 3311 3.393941 TGTTACCCTACCCGGAAAGAAAA 59.606 43.478 0.73 0.00 33.16 2.29
1958 3313 2.618794 TGTTACCCTACCCGGAAAGAA 58.381 47.619 0.73 0.00 33.16 2.52
1960 3315 2.303890 ACTTGTTACCCTACCCGGAAAG 59.696 50.000 0.73 0.00 33.16 2.62
1962 3317 2.028561 ACTTGTTACCCTACCCGGAA 57.971 50.000 0.73 0.00 33.16 4.30
1964 3319 2.616256 GGAAACTTGTTACCCTACCCGG 60.616 54.545 0.00 0.00 0.00 5.73
1965 3320 2.303890 AGGAAACTTGTTACCCTACCCG 59.696 50.000 5.84 0.00 37.44 5.28
1967 3322 5.868454 TGTTAGGAAACTTGTTACCCTACC 58.132 41.667 11.48 7.68 43.67 3.18
2054 3542 3.872511 TGTTCATCATGAATTGGTGCC 57.127 42.857 2.67 0.00 38.79 5.01
2156 3742 9.542462 CACGAAATCTAGTCCCTGAATTAATTA 57.458 33.333 0.00 0.00 0.00 1.40
2157 3743 8.265055 TCACGAAATCTAGTCCCTGAATTAATT 58.735 33.333 0.00 0.00 0.00 1.40
2230 3816 2.107366 CCAAACTCACCCCAGTTGTTT 58.893 47.619 0.00 0.00 36.69 2.83
2245 3890 2.812358 ATTGTTTCTTCCCGCCAAAC 57.188 45.000 0.00 0.00 0.00 2.93
2339 3984 5.241506 CCTTGATGTGGTTCATGTACAAGTT 59.758 40.000 0.00 0.00 35.73 2.66
2376 4021 1.556564 AGCGATACACGTGCATGTAC 58.443 50.000 17.22 3.51 44.60 2.90
2377 4022 3.423996 TTAGCGATACACGTGCATGTA 57.576 42.857 17.22 6.95 44.60 2.29
2378 4023 2.287393 TTAGCGATACACGTGCATGT 57.713 45.000 17.22 5.51 44.60 3.21
2380 4025 5.164090 CGATTAATTAGCGATACACGTGCAT 60.164 40.000 17.22 8.59 44.60 3.96
2381 4026 4.147479 CGATTAATTAGCGATACACGTGCA 59.853 41.667 17.22 2.06 44.60 4.57
2382 4027 4.615386 CGATTAATTAGCGATACACGTGC 58.385 43.478 17.22 0.00 44.60 5.34
2384 4029 4.880760 GCGATTAATTAGCGATACACGT 57.119 40.909 12.28 0.00 44.60 4.49
2393 4038 2.348591 GGAGTGCACGCGATTAATTAGC 60.349 50.000 15.93 3.89 0.00 3.09
2395 4040 2.206750 GGGAGTGCACGCGATTAATTA 58.793 47.619 15.93 0.00 0.00 1.40
2396 4041 1.014352 GGGAGTGCACGCGATTAATT 58.986 50.000 15.93 0.00 0.00 1.40
2397 4042 1.151777 CGGGAGTGCACGCGATTAAT 61.152 55.000 15.93 0.00 46.30 1.40
2416 4069 7.366461 CACGCGATTAGTTTAAGTTTATTCGAC 59.634 37.037 15.93 0.00 0.00 4.20
2428 4081 1.392168 GCAGTGCACGCGATTAGTTTA 59.608 47.619 15.93 0.00 0.00 2.01
2429 4082 0.165944 GCAGTGCACGCGATTAGTTT 59.834 50.000 15.93 0.00 0.00 2.66
2430 4083 0.948623 TGCAGTGCACGCGATTAGTT 60.949 50.000 15.37 0.00 31.71 2.24
2431 4084 0.740868 ATGCAGTGCACGCGATTAGT 60.741 50.000 22.44 0.00 43.04 2.24
2432 4085 0.315625 CATGCAGTGCACGCGATTAG 60.316 55.000 22.44 0.00 43.04 1.73
2433 4086 1.018752 ACATGCAGTGCACGCGATTA 61.019 50.000 22.44 10.24 43.04 1.75
2454 4107 1.491563 CTTAACGTGACGGCAGTGC 59.508 57.895 10.66 6.55 0.00 4.40
2533 4223 4.396790 GGTGCATATCCAAGGAAAAACGTA 59.603 41.667 0.00 0.00 0.00 3.57
2542 4232 3.260884 ACCTATACGGTGCATATCCAAGG 59.739 47.826 0.00 0.00 46.80 3.61
2562 4256 8.123445 AGTTAACGATCGACACAAAATATACC 57.877 34.615 24.34 0.00 0.00 2.73
2564 4258 9.577110 AAGAGTTAACGATCGACACAAAATATA 57.423 29.630 24.34 0.00 0.00 0.86
2567 4261 6.202188 ACAAGAGTTAACGATCGACACAAAAT 59.798 34.615 24.34 7.17 0.00 1.82
2568 4262 5.521010 ACAAGAGTTAACGATCGACACAAAA 59.479 36.000 24.34 3.47 0.00 2.44
2570 4264 4.443063 CACAAGAGTTAACGATCGACACAA 59.557 41.667 24.34 6.73 0.00 3.33
2571 4265 3.978855 CACAAGAGTTAACGATCGACACA 59.021 43.478 24.34 0.02 0.00 3.72
2572 4266 3.979495 ACACAAGAGTTAACGATCGACAC 59.021 43.478 24.34 14.37 0.00 3.67
2573 4267 4.233123 ACACAAGAGTTAACGATCGACA 57.767 40.909 24.34 5.65 0.00 4.35
2574 4268 5.149273 TGTACACAAGAGTTAACGATCGAC 58.851 41.667 24.34 9.91 0.00 4.20
2575 4269 5.361135 TGTACACAAGAGTTAACGATCGA 57.639 39.130 24.34 0.00 0.00 3.59
2576 4270 5.571741 ACATGTACACAAGAGTTAACGATCG 59.428 40.000 14.88 14.88 0.00 3.69
2577 4271 6.365247 ACACATGTACACAAGAGTTAACGATC 59.635 38.462 0.00 0.00 0.00 3.69
2578 4272 6.145534 CACACATGTACACAAGAGTTAACGAT 59.854 38.462 0.00 0.00 0.00 3.73
2597 4291 0.546267 ACCCTCTGCTCTCCACACAT 60.546 55.000 0.00 0.00 0.00 3.21
2623 4317 1.867233 CCCGTGAAGTTGTTGACTCTG 59.133 52.381 0.00 0.00 37.72 3.35
2950 4780 3.378112 TGTTCTTGTGTGGCTTCTCTTTG 59.622 43.478 0.00 0.00 0.00 2.77
2955 4785 4.646492 AGAAAATGTTCTTGTGTGGCTTCT 59.354 37.500 0.00 0.00 41.55 2.85
2956 4786 4.741676 CAGAAAATGTTCTTGTGTGGCTTC 59.258 41.667 0.00 0.00 41.55 3.86
2957 4787 4.160252 ACAGAAAATGTTCTTGTGTGGCTT 59.840 37.500 0.00 0.00 41.55 4.35
2958 4788 3.701040 ACAGAAAATGTTCTTGTGTGGCT 59.299 39.130 0.00 0.00 41.55 4.75
2959 4789 4.044426 GACAGAAAATGTTCTTGTGTGGC 58.956 43.478 0.00 0.00 44.17 5.01
2960 4790 5.247507 TGACAGAAAATGTTCTTGTGTGG 57.752 39.130 0.00 0.00 44.17 4.17
2961 4791 4.736793 GCTGACAGAAAATGTTCTTGTGTG 59.263 41.667 6.65 0.00 44.17 3.82
2962 4792 4.202050 GGCTGACAGAAAATGTTCTTGTGT 60.202 41.667 6.65 0.00 44.17 3.72
2963 4793 4.293415 GGCTGACAGAAAATGTTCTTGTG 58.707 43.478 6.65 0.00 44.17 3.33
2964 4794 3.319122 GGGCTGACAGAAAATGTTCTTGT 59.681 43.478 6.65 0.00 44.17 3.16
2965 4795 3.571401 AGGGCTGACAGAAAATGTTCTTG 59.429 43.478 6.65 0.00 44.17 3.02
2969 4808 3.228188 TCAGGGCTGACAGAAAATGTT 57.772 42.857 6.65 0.00 44.17 2.71
2979 4818 1.541233 CCATCGGTTATCAGGGCTGAC 60.541 57.143 0.00 0.00 43.11 3.51
3020 4870 1.062365 CACACACACAAGCCACACG 59.938 57.895 0.00 0.00 0.00 4.49
3024 4874 0.747644 CCTGACACACACACAAGCCA 60.748 55.000 0.00 0.00 0.00 4.75
3025 4875 1.447317 CCCTGACACACACACAAGCC 61.447 60.000 0.00 0.00 0.00 4.35
3026 4876 0.748005 ACCCTGACACACACACAAGC 60.748 55.000 0.00 0.00 0.00 4.01
3027 4877 1.016627 CACCCTGACACACACACAAG 58.983 55.000 0.00 0.00 0.00 3.16
3028 4878 1.029408 GCACCCTGACACACACACAA 61.029 55.000 0.00 0.00 0.00 3.33
3029 4879 1.451207 GCACCCTGACACACACACA 60.451 57.895 0.00 0.00 0.00 3.72
3058 4908 4.074526 TCCACCTGCTGCTCGCTC 62.075 66.667 0.00 0.00 40.11 5.03
3206 5062 1.135315 GTAGATGGCGTCGTACACCAA 60.135 52.381 0.13 0.00 33.52 3.67
3261 5117 0.607489 CAACACCTGCCAGAAGAGGG 60.607 60.000 0.00 0.00 33.16 4.30
3350 5206 2.888863 GCACTCCTGGGAGACGAG 59.111 66.667 21.86 10.16 44.53 4.18
3381 5237 1.736032 GCTAGACTCACGGCGTGATTT 60.736 52.381 38.91 29.16 41.94 2.17
3481 5355 5.179368 CCGATTGCAATTATCCTAACACGAT 59.821 40.000 14.33 0.00 0.00 3.73
3495 5369 3.874543 TGACGTAATTAGCCGATTGCAAT 59.125 39.130 12.83 12.83 44.83 3.56
3552 5429 1.707989 TCCCTTTCTTGGTATGCCACA 59.292 47.619 0.24 0.00 46.01 4.17
3627 5504 7.476540 AACCTATGGGTCCTTTACAAAAATC 57.523 36.000 0.00 0.00 46.67 2.17
3634 5511 6.002653 AGATGAAACCTATGGGTCCTTTAC 57.997 41.667 0.00 0.00 46.67 2.01
3673 5550 0.605589 GAAGTTGGACGAAGGGGTGG 60.606 60.000 0.00 0.00 0.00 4.61
3695 5572 3.009584 GCTAGAAGGGGATGGGAAATAGG 59.990 52.174 0.00 0.00 0.00 2.57
3697 5574 3.954662 AGCTAGAAGGGGATGGGAAATA 58.045 45.455 0.00 0.00 0.00 1.40
3814 5691 1.026182 TGTGCCCGTGATTGATCTGC 61.026 55.000 0.00 0.00 0.00 4.26
3906 5783 6.049149 ACACAATAAGATGTCCATACGAAGG 58.951 40.000 0.00 0.00 0.00 3.46
3939 5816 5.170021 GCATTGCTATGTGGATCAAACAAA 58.830 37.500 9.87 0.00 34.12 2.83
3940 5817 4.220163 TGCATTGCTATGTGGATCAAACAA 59.780 37.500 10.49 0.00 34.12 2.83
3995 5872 1.069668 GAGTGTGTTTCTACCACCGGT 59.930 52.381 0.00 0.00 40.16 5.28
3996 5873 1.607251 GGAGTGTGTTTCTACCACCGG 60.607 57.143 0.00 0.00 31.71 5.28
4034 5911 6.068473 AGAAACGAAAAACATACTTGTCCC 57.932 37.500 0.00 0.00 34.06 4.46
4043 5920 8.889717 TCAAGAGAGTTTAGAAACGAAAAACAT 58.110 29.630 0.00 0.00 43.51 2.71
4064 5941 7.279981 TGAGAGACGATTTTTGAACTTTCAAGA 59.720 33.333 4.66 0.00 46.68 3.02
4068 5945 7.410485 AGTTGAGAGACGATTTTTGAACTTTC 58.590 34.615 0.00 0.00 0.00 2.62
4075 5952 7.044052 GGTTTTGAAGTTGAGAGACGATTTTTG 60.044 37.037 0.00 0.00 0.00 2.44
4083 5960 3.627577 TGCTGGTTTTGAAGTTGAGAGAC 59.372 43.478 0.00 0.00 0.00 3.36
4086 5963 5.047377 AGTTTTGCTGGTTTTGAAGTTGAGA 60.047 36.000 0.00 0.00 0.00 3.27
4120 5997 9.099454 GACGAAGATTATCTGGTTTCAATAGTT 57.901 33.333 0.00 0.00 0.00 2.24
4125 6002 6.049955 AGGACGAAGATTATCTGGTTTCAA 57.950 37.500 0.00 0.00 0.00 2.69
4145 6022 8.719596 TCAAACCACCTAAAGCATTATATAGGA 58.280 33.333 4.78 0.00 38.61 2.94
4155 6032 3.810941 CGTTACTCAAACCACCTAAAGCA 59.189 43.478 0.00 0.00 34.33 3.91
4157 6034 5.051816 TCACGTTACTCAAACCACCTAAAG 58.948 41.667 0.00 0.00 34.33 1.85
4164 6041 2.563702 GGGTTCACGTTACTCAAACCA 58.436 47.619 10.29 0.00 40.92 3.67
4168 6045 0.752054 ACCGGGTTCACGTTACTCAA 59.248 50.000 6.32 0.00 0.00 3.02
4180 6059 7.226441 ACTAGTATTTAGTCAAAAACCGGGTT 58.774 34.615 6.59 6.59 0.00 4.11
4189 6068 6.094881 GGCCATGCAACTAGTATTTAGTCAAA 59.905 38.462 0.00 0.00 0.00 2.69
4202 6081 2.101783 CAAATCCAGGCCATGCAACTA 58.898 47.619 5.01 0.00 0.00 2.24
4205 6084 0.896923 GTCAAATCCAGGCCATGCAA 59.103 50.000 5.01 0.00 0.00 4.08
4206 6085 0.971959 GGTCAAATCCAGGCCATGCA 60.972 55.000 5.01 0.00 0.00 3.96
4207 6086 0.971959 TGGTCAAATCCAGGCCATGC 60.972 55.000 5.01 0.00 33.19 4.06
4218 6097 2.341846 AACTGACGTGGTGGTCAAAT 57.658 45.000 0.00 0.00 45.59 2.32
4246 6125 1.640917 TAGAAGCGTGAGGGTCCTTT 58.359 50.000 0.00 0.00 0.00 3.11
4284 6163 2.490902 GGTTTGTCAGAAAGGGGGTGAT 60.491 50.000 0.00 0.00 0.00 3.06
4286 6165 1.328279 GGTTTGTCAGAAAGGGGGTG 58.672 55.000 0.00 0.00 0.00 4.61
4287 6166 0.187606 GGGTTTGTCAGAAAGGGGGT 59.812 55.000 0.00 0.00 0.00 4.95
4288 6167 0.482887 AGGGTTTGTCAGAAAGGGGG 59.517 55.000 0.00 0.00 0.00 5.40
4297 6176 3.844211 AGCTATAGGTTCAGGGTTTGTCA 59.156 43.478 0.00 0.00 0.00 3.58
4308 6187 1.962100 ACCACCGCTAGCTATAGGTTC 59.038 52.381 13.93 2.08 34.25 3.62
4315 6194 2.412323 CCGTCACCACCGCTAGCTA 61.412 63.158 13.93 0.00 0.00 3.32
4323 6202 2.388232 GCGAATCACCGTCACCACC 61.388 63.158 0.00 0.00 0.00 4.61
4325 6204 1.080093 GAGCGAATCACCGTCACCA 60.080 57.895 0.00 0.00 0.00 4.17
4340 6219 3.818787 CCGCTGCAACCCATGAGC 61.819 66.667 0.00 0.00 0.00 4.26
4361 6240 2.176273 CGTAGCCATGCCTCAGTGC 61.176 63.158 0.00 0.00 0.00 4.40
4371 6250 2.268920 CACCAGTGCCGTAGCCAT 59.731 61.111 0.00 0.00 38.69 4.40
4383 6262 4.293648 TGGACACGTCGCCACCAG 62.294 66.667 1.87 0.00 0.00 4.00
4384 6263 4.293648 CTGGACACGTCGCCACCA 62.294 66.667 1.87 0.00 0.00 4.17
4396 6275 1.810412 CGCCTAAATAGCCACCTGGAC 60.810 57.143 0.00 0.00 37.39 4.02
4400 6279 0.463833 GCACGCCTAAATAGCCACCT 60.464 55.000 0.00 0.00 0.00 4.00
4401 6280 0.463833 AGCACGCCTAAATAGCCACC 60.464 55.000 0.00 0.00 0.00 4.61
4407 6286 0.906066 TCCACCAGCACGCCTAAATA 59.094 50.000 0.00 0.00 0.00 1.40
4419 6298 1.259609 ATGCAACAACCATCCACCAG 58.740 50.000 0.00 0.00 0.00 4.00
4469 6348 8.210946 TGGAATCAAGGTCGATATTAATGACTT 58.789 33.333 0.00 0.00 33.21 3.01
4473 6352 8.090831 TCTCTGGAATCAAGGTCGATATTAATG 58.909 37.037 0.00 0.00 0.00 1.90
4475 6354 7.597288 TCTCTGGAATCAAGGTCGATATTAA 57.403 36.000 0.00 0.00 0.00 1.40
4476 6355 7.782897 ATCTCTGGAATCAAGGTCGATATTA 57.217 36.000 0.00 0.00 0.00 0.98
4479 6358 7.782897 ATTATCTCTGGAATCAAGGTCGATA 57.217 36.000 0.00 0.00 0.00 2.92
4481 6360 6.485830 AATTATCTCTGGAATCAAGGTCGA 57.514 37.500 0.00 0.00 0.00 4.20
4502 6381 8.930846 AGATTGCAATGACTATAGGCTAAAAT 57.069 30.769 18.59 0.23 0.00 1.82
4559 6438 6.096673 TGCATACAAGAGAGACAAACACTA 57.903 37.500 0.00 0.00 0.00 2.74
4581 6460 5.960811 AGGATCCATGTGACTACCCTATATG 59.039 44.000 15.82 0.00 0.00 1.78
4604 6483 8.567285 AAATCTAATAAACAACACCTCTCCAG 57.433 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.