Multiple sequence alignment - TraesCS1B01G045100

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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 TraesCS1B01G045100 chr1B 100.000 2534 0 0 1 2534 24990051 24987518 0.000000e+00 4680.0
1 TraesCS1B01G045100 chr1D 87.958 2101 136 43 261 2328 17194683 17192667 0.000000e+00 2370.0
2 TraesCS1B01G045100 chr1D 88.532 218 23 2 35 251 17196255 17196039 1.930000e-66 263.0
3 TraesCS1B01G045100 chr1D 100.000 39 0 0 1 39 17196438 17196400 3.500000e-09 73.1
4 TraesCS1B01G045100 chr1A 90.155 1290 77 14 261 1540 18487739 18486490 0.000000e+00 1633.0
5 TraesCS1B01G045100 chr1A 85.681 859 60 28 1509 2336 18486466 18485640 0.000000e+00 846.0
6 TraesCS1B01G045100 chr1A 86.047 215 28 2 37 250 18489111 18488898 1.960000e-56 230.0
7 TraesCS1B01G045100 chr1A 97.436 39 1 0 1 39 18489301 18489263 1.630000e-07 67.6
8 TraesCS1B01G045100 chr5B 85.592 583 66 9 1001 1581 612015077 612014511 1.680000e-166 595.0
9 TraesCS1B01G045100 chr3D 84.091 572 74 11 1001 1571 438604264 438603709 1.030000e-148 536.0
10 TraesCS1B01G045100 chr5D 84.286 560 67 9 1024 1581 495373539 495372999 6.210000e-146 527.0
11 TraesCS1B01G045100 chr5A 80.845 663 83 17 943 1603 619476694 619476074 4.900000e-132 481.0


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 TraesCS1B01G045100 chr1B 24987518 24990051 2533 True 4680.000000 4680 100.000000 1 2534 1 chr1B.!!$R1 2533
1 TraesCS1B01G045100 chr1D 17192667 17196438 3771 True 902.033333 2370 92.163333 1 2328 3 chr1D.!!$R1 2327
2 TraesCS1B01G045100 chr1A 18485640 18489301 3661 True 694.150000 1633 89.829750 1 2336 4 chr1A.!!$R1 2335
3 TraesCS1B01G045100 chr5B 612014511 612015077 566 True 595.000000 595 85.592000 1001 1581 1 chr5B.!!$R1 580
4 TraesCS1B01G045100 chr3D 438603709 438604264 555 True 536.000000 536 84.091000 1001 1571 1 chr3D.!!$R1 570
5 TraesCS1B01G045100 chr5D 495372999 495373539 540 True 527.000000 527 84.286000 1024 1581 1 chr5D.!!$R1 557
6 TraesCS1B01G045100 chr5A 619476074 619476694 620 True 481.000000 481 80.845000 943 1603 1 chr5A.!!$R1 660

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
48 205 0.108472 TGCTTCCGTGAGAGCAGATG 60.108 55.0 0.0 0.0 33.06 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 3609 0.036732 CACCTAACTCAAGGCCAGCA 59.963 55.0 5.01 0.0 40.62 4.41 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
48 205 0.108472 TGCTTCCGTGAGAGCAGATG 60.108 55.000 0.00 0.00 33.06 2.90
64 221 3.644823 CAGATGTGCATTGCTTCAACAA 58.355 40.909 10.49 0.00 0.00 2.83
74 231 7.373966 GTGCATTGCTTCAACAAGTTTTATTTG 59.626 33.333 10.49 0.00 31.96 2.32
86 243 3.634910 AGTTTTATTTGTTCCACGGTGCT 59.365 39.130 1.68 0.00 0.00 4.40
105 262 6.456988 CGGTGCTGATTAATTCCTAGTCAAAC 60.457 42.308 0.00 0.00 0.00 2.93
114 272 6.877611 AATTCCTAGTCAAACAACGTCAAT 57.122 33.333 0.00 0.00 0.00 2.57
117 275 7.972832 TTCCTAGTCAAACAACGTCAATAAT 57.027 32.000 0.00 0.00 0.00 1.28
130 288 8.752254 ACAACGTCAATAATCTGTCGTATATTG 58.248 33.333 0.00 0.00 39.56 1.90
163 321 5.835257 AGTGTGCATATATTCACAAATGGC 58.165 37.500 18.00 7.22 43.78 4.40
170 329 7.985752 TGCATATATTCACAAATGGCAAAATCA 59.014 29.630 0.00 0.00 0.00 2.57
231 390 5.681982 GGACAGAATTACATAAGTCGAGTCG 59.318 44.000 6.09 6.09 39.11 4.18
236 395 1.183549 ACATAAGTCGAGTCGGGCTT 58.816 50.000 20.73 20.73 0.00 4.35
369 1878 1.604378 CCAAATCGCCTCCCACTCT 59.396 57.895 0.00 0.00 0.00 3.24
387 1896 0.736672 CTCTCGACGTCGACTCTGGA 60.737 60.000 34.97 27.00 44.22 3.86
396 1905 1.000771 CGACTCTGGACTCTGGGGA 60.001 63.158 0.00 0.00 0.00 4.81
412 1921 2.577059 GATGTCACCGAGGCCGAA 59.423 61.111 0.00 0.00 38.22 4.30
431 1940 1.562783 AGGTGCCTCTAGGACTCAAC 58.437 55.000 0.00 0.00 37.39 3.18
432 1941 1.077993 AGGTGCCTCTAGGACTCAACT 59.922 52.381 0.00 0.00 37.39 3.16
433 1942 1.478916 GGTGCCTCTAGGACTCAACTC 59.521 57.143 0.00 0.00 37.39 3.01
434 1943 2.171840 GTGCCTCTAGGACTCAACTCA 58.828 52.381 0.00 0.00 37.39 3.41
435 1944 2.563179 GTGCCTCTAGGACTCAACTCAA 59.437 50.000 0.00 0.00 37.39 3.02
436 1945 2.828520 TGCCTCTAGGACTCAACTCAAG 59.171 50.000 0.00 0.00 37.39 3.02
437 1946 2.167487 GCCTCTAGGACTCAACTCAAGG 59.833 54.545 0.00 0.00 37.39 3.61
438 1947 3.702792 CCTCTAGGACTCAACTCAAGGA 58.297 50.000 0.00 0.00 37.39 3.36
439 1948 3.699038 CCTCTAGGACTCAACTCAAGGAG 59.301 52.174 0.00 0.00 37.39 3.69
475 1988 1.206371 GGCTTACTTCCCGAGCAGTTA 59.794 52.381 0.00 0.00 38.14 2.24
476 1989 2.541556 GCTTACTTCCCGAGCAGTTAG 58.458 52.381 0.00 0.00 36.45 2.34
477 1990 2.094130 GCTTACTTCCCGAGCAGTTAGT 60.094 50.000 0.00 0.00 36.45 2.24
478 1991 3.616802 GCTTACTTCCCGAGCAGTTAGTT 60.617 47.826 0.00 0.00 36.45 2.24
479 1992 4.566987 CTTACTTCCCGAGCAGTTAGTTT 58.433 43.478 0.00 0.00 0.00 2.66
480 1993 5.717119 CTTACTTCCCGAGCAGTTAGTTTA 58.283 41.667 0.00 0.00 0.00 2.01
481 1994 4.820894 ACTTCCCGAGCAGTTAGTTTAT 57.179 40.909 0.00 0.00 0.00 1.40
482 1995 5.161943 ACTTCCCGAGCAGTTAGTTTATT 57.838 39.130 0.00 0.00 0.00 1.40
483 1996 5.557866 ACTTCCCGAGCAGTTAGTTTATTT 58.442 37.500 0.00 0.00 0.00 1.40
492 2014 5.869888 AGCAGTTAGTTTATTTCTCTGTCCG 59.130 40.000 0.00 0.00 0.00 4.79
536 2058 6.127814 CCAGTCTGATTGTTTCATGCAGTATT 60.128 38.462 0.00 0.00 32.72 1.89
569 2091 2.014128 CGTGGTATGGGTTTGTGATCC 58.986 52.381 0.00 0.00 0.00 3.36
607 2139 5.983720 GCGTCCATTCTAGCTGAACTTATAA 59.016 40.000 0.00 0.00 37.52 0.98
608 2140 6.647067 GCGTCCATTCTAGCTGAACTTATAAT 59.353 38.462 0.00 0.00 37.52 1.28
633 2165 6.040209 TGATGAATGGTTTGCTTGCTTAAT 57.960 33.333 0.00 0.00 0.00 1.40
655 2187 2.213499 CTTAGCTAAATCCGTGGGCTG 58.787 52.381 7.74 0.00 34.88 4.85
666 2198 1.804748 CCGTGGGCTGTCTTTACTTTC 59.195 52.381 0.00 0.00 0.00 2.62
677 2209 6.539103 GCTGTCTTTACTTTCCTTATGTAGGG 59.461 42.308 0.00 0.00 44.86 3.53
695 2227 6.001460 TGTAGGGAAGGTGTTTGATAAAGTG 58.999 40.000 0.00 0.00 0.00 3.16
734 2266 2.393764 CGAATGGGTGCTTTGTTGTTC 58.606 47.619 0.00 0.00 0.00 3.18
735 2267 2.223688 CGAATGGGTGCTTTGTTGTTCA 60.224 45.455 0.00 0.00 0.00 3.18
767 2299 7.052565 TCCAGTTAATTACTTTAAACTCGCG 57.947 36.000 0.00 0.00 33.85 5.87
782 2314 0.600557 TCGCGCATGGTTTCCAAAAT 59.399 45.000 8.75 0.00 36.95 1.82
805 2337 1.452651 CCTGCCACATCGCATCCTT 60.453 57.895 0.00 0.00 38.30 3.36
806 2338 1.033746 CCTGCCACATCGCATCCTTT 61.034 55.000 0.00 0.00 38.30 3.11
813 2345 2.485426 CACATCGCATCCTTTGTTCAGT 59.515 45.455 0.00 0.00 0.00 3.41
842 2374 1.016627 TGCAGCAACTTCACTGTGTC 58.983 50.000 7.79 0.00 36.26 3.67
924 2456 7.553881 TTGAAAGGTATAACAAGCTATGCTC 57.446 36.000 0.00 0.00 38.25 4.26
925 2457 6.889198 TGAAAGGTATAACAAGCTATGCTCT 58.111 36.000 0.00 0.00 38.25 4.09
926 2458 7.338710 TGAAAGGTATAACAAGCTATGCTCTT 58.661 34.615 0.00 0.00 38.25 2.85
927 2459 8.482943 TGAAAGGTATAACAAGCTATGCTCTTA 58.517 33.333 0.00 0.00 38.25 2.10
953 2485 4.455533 TCTTACAGCTGTGCAGGTTAATTG 59.544 41.667 29.57 3.18 36.98 2.32
1038 2570 7.701539 TGTTTGCAGGAAGTTGTATGATTAT 57.298 32.000 0.00 0.00 0.00 1.28
1119 2651 0.749649 AGAGGCATCCTAAGCTCACG 59.250 55.000 0.00 0.00 31.76 4.35
1137 2669 1.537202 ACGCTGAAAGAGAAATGGTGC 59.463 47.619 0.00 0.00 37.13 5.01
1233 2765 6.467677 TGATTACAAGAAGGTCAAAGAGGAG 58.532 40.000 0.00 0.00 0.00 3.69
1251 2783 0.610687 AGTCTGACCCTAACAGCAGC 59.389 55.000 3.76 0.00 35.61 5.25
1252 2784 0.321671 GTCTGACCCTAACAGCAGCA 59.678 55.000 0.00 0.00 35.61 4.41
1253 2785 1.055849 TCTGACCCTAACAGCAGCAA 58.944 50.000 0.00 0.00 35.61 3.91
1254 2786 1.002430 TCTGACCCTAACAGCAGCAAG 59.998 52.381 0.00 0.00 35.61 4.01
1255 2787 0.036732 TGACCCTAACAGCAGCAAGG 59.963 55.000 0.00 0.00 0.00 3.61
1275 2810 1.949079 GCCAAGGAGGGGAAAACTACG 60.949 57.143 0.00 0.00 38.09 3.51
1278 2813 0.903236 AGGAGGGGAAAACTACGAGC 59.097 55.000 0.00 0.00 0.00 5.03
1288 2823 1.015868 AACTACGAGCGAGCCTAGTC 58.984 55.000 0.00 0.00 31.50 2.59
1371 2906 1.955529 GCATATACATGACCCGCGCG 61.956 60.000 25.67 25.67 33.67 6.86
1446 2981 5.494724 CTGAAGGATGTCTTGGATGAGAAA 58.505 41.667 0.00 0.00 35.50 2.52
1507 3103 4.592192 CATCGACGCCGCCTCCAT 62.592 66.667 0.00 0.00 35.37 3.41
1571 3169 6.605594 TGTGGGGAAATGTTATCATTAGAACC 59.394 38.462 0.00 2.27 42.60 3.62
1592 3190 3.673809 CCCGCAGCTTCTCGTTTATATAC 59.326 47.826 0.00 0.00 0.00 1.47
1594 3192 4.923871 CCGCAGCTTCTCGTTTATATACAT 59.076 41.667 0.00 0.00 0.00 2.29
1621 3219 2.295349 TCACAAGTCGGGTAGAACAGAC 59.705 50.000 0.00 0.00 0.00 3.51
1625 3223 2.313317 AGTCGGGTAGAACAGACAACA 58.687 47.619 0.73 0.00 36.18 3.33
1637 3235 1.510623 GACAACAATGCGCTGCTCG 60.511 57.895 9.73 0.00 42.12 5.03
1641 3239 0.871722 AACAATGCGCTGCTCGTTTA 59.128 45.000 9.73 0.00 41.07 2.01
1642 3240 1.086696 ACAATGCGCTGCTCGTTTAT 58.913 45.000 9.73 0.00 41.07 1.40
1643 3241 2.276201 ACAATGCGCTGCTCGTTTATA 58.724 42.857 9.73 0.00 41.07 0.98
1644 3242 2.872245 ACAATGCGCTGCTCGTTTATAT 59.128 40.909 9.73 0.00 41.07 0.86
1646 3244 4.690748 ACAATGCGCTGCTCGTTTATATAT 59.309 37.500 9.73 0.00 41.07 0.86
1648 3246 4.903638 TGCGCTGCTCGTTTATATATTC 57.096 40.909 9.73 0.00 41.07 1.75
1649 3247 4.556233 TGCGCTGCTCGTTTATATATTCT 58.444 39.130 9.73 0.00 41.07 2.40
1650 3248 4.988540 TGCGCTGCTCGTTTATATATTCTT 59.011 37.500 9.73 0.00 41.07 2.52
1652 3250 6.811665 TGCGCTGCTCGTTTATATATTCTTAT 59.188 34.615 9.73 0.00 41.07 1.73
1653 3251 7.009265 TGCGCTGCTCGTTTATATATTCTTATC 59.991 37.037 9.73 0.00 41.07 1.75
1654 3252 7.221067 GCGCTGCTCGTTTATATATTCTTATCT 59.779 37.037 0.00 0.00 41.07 1.98
1655 3253 8.527488 CGCTGCTCGTTTATATATTCTTATCTG 58.473 37.037 0.00 0.00 0.00 2.90
1656 3254 9.574458 GCTGCTCGTTTATATATTCTTATCTGA 57.426 33.333 0.00 0.00 0.00 3.27
1658 3256 9.856488 TGCTCGTTTATATATTCTTATCTGACC 57.144 33.333 0.00 0.00 0.00 4.02
1716 3345 0.793250 GTTCTTCAGCTTGTCTCGGC 59.207 55.000 0.00 0.00 0.00 5.54
1760 3389 4.412933 TCGAAATCGACGCCATCC 57.587 55.556 0.58 0.00 44.22 3.51
1764 3393 0.179084 GAAATCGACGCCATCCAGGA 60.179 55.000 0.00 0.00 41.22 3.86
1783 3412 0.457035 ACTGTGTGCTTGCCTTGTTG 59.543 50.000 0.00 0.00 0.00 3.33
1784 3413 0.872881 CTGTGTGCTTGCCTTGTTGC 60.873 55.000 0.00 0.00 0.00 4.17
1785 3414 1.321805 TGTGTGCTTGCCTTGTTGCT 61.322 50.000 0.00 0.00 0.00 3.91
1786 3415 0.667993 GTGTGCTTGCCTTGTTGCTA 59.332 50.000 0.00 0.00 0.00 3.49
1787 3416 0.953727 TGTGCTTGCCTTGTTGCTAG 59.046 50.000 0.00 0.00 37.20 3.42
1825 3454 2.428530 GGCCCATCCTGTCATTTTCTTC 59.571 50.000 0.00 0.00 0.00 2.87
1830 3459 4.637534 CCATCCTGTCATTTTCTTCGATGT 59.362 41.667 0.00 0.00 0.00 3.06
1831 3460 5.817296 CCATCCTGTCATTTTCTTCGATGTA 59.183 40.000 0.00 0.00 0.00 2.29
1869 3498 2.415090 CCTCGATCGTCGTTGGTACTTT 60.415 50.000 15.94 0.00 41.35 2.66
1870 3499 2.587956 TCGATCGTCGTTGGTACTTTG 58.412 47.619 15.94 0.00 41.35 2.77
1871 3500 2.030893 TCGATCGTCGTTGGTACTTTGT 60.031 45.455 15.94 0.00 41.35 2.83
1872 3501 2.727798 CGATCGTCGTTGGTACTTTGTT 59.272 45.455 7.03 0.00 34.72 2.83
1980 3609 4.694509 GTCTCTGATCTTGTTCATGTGCTT 59.305 41.667 0.00 0.00 0.00 3.91
2065 3694 2.237392 GAGGTCTGCCATACCATATCCC 59.763 54.545 1.78 0.00 39.64 3.85
2073 3702 5.826643 TGCCATACCATATCCCCTAATTTC 58.173 41.667 0.00 0.00 0.00 2.17
2131 3760 2.322161 CAAACACAGTATGCTTGCTGC 58.678 47.619 16.04 0.00 42.53 5.25
2132 3761 1.901591 AACACAGTATGCTTGCTGCT 58.098 45.000 16.04 3.05 42.53 4.24
2148 3777 6.505044 TTGCTGCTCATGGCTTATTATATG 57.495 37.500 0.00 0.00 42.39 1.78
2176 3805 1.418637 GGTCGCCATATAGTCCCCAAA 59.581 52.381 0.00 0.00 0.00 3.28
2177 3806 2.490991 GTCGCCATATAGTCCCCAAAC 58.509 52.381 0.00 0.00 0.00 2.93
2178 3807 1.418637 TCGCCATATAGTCCCCAAACC 59.581 52.381 0.00 0.00 0.00 3.27
2179 3808 1.420138 CGCCATATAGTCCCCAAACCT 59.580 52.381 0.00 0.00 0.00 3.50
2191 3820 9.900112 ATAGTCCCCAAACCTATCTATATATCC 57.100 37.037 0.00 0.00 0.00 2.59
2201 3830 9.944079 AACCTATCTATATATCCAGCAGTACAT 57.056 33.333 0.00 0.00 0.00 2.29
2216 3845 5.295292 AGCAGTACATGTTACTGATTGATGC 59.705 40.000 26.22 16.05 45.69 3.91
2241 3870 3.363673 GCTTAGTCGTGGTTGCTGTAAAC 60.364 47.826 0.00 0.00 0.00 2.01
2254 3883 3.056607 TGCTGTAAACGGTAGGTCTAACC 60.057 47.826 0.00 0.00 38.99 2.85
2266 3895 2.239150 AGGTCTAACCAGCTCGTCTCTA 59.761 50.000 0.00 0.00 41.95 2.43
2274 3903 1.139947 GCTCGTCTCTACAGTGCCC 59.860 63.158 0.00 0.00 0.00 5.36
2276 3905 1.994507 CTCGTCTCTACAGTGCCCGG 61.995 65.000 0.00 0.00 0.00 5.73
2306 3935 4.332637 CACTGGGCTGCAACGTGC 62.333 66.667 0.50 0.00 45.29 5.34
2319 3948 0.179078 AACGTGCCGAAACTGTACCA 60.179 50.000 0.00 0.00 0.00 3.25
2328 3957 1.671845 GAAACTGTACCACAACCGCAA 59.328 47.619 0.00 0.00 0.00 4.85
2331 3960 2.250190 GTACCACAACCGCAACGC 59.750 61.111 0.00 0.00 0.00 4.84
2336 3965 2.203015 ACAACCGCAACGCAGTCT 60.203 55.556 0.00 0.00 45.00 3.24
2337 3966 1.068417 ACAACCGCAACGCAGTCTA 59.932 52.632 0.00 0.00 45.00 2.59
2338 3967 0.531090 ACAACCGCAACGCAGTCTAA 60.531 50.000 0.00 0.00 45.00 2.10
2339 3968 0.796312 CAACCGCAACGCAGTCTAAT 59.204 50.000 0.00 0.00 45.00 1.73
2340 3969 1.076332 AACCGCAACGCAGTCTAATC 58.924 50.000 0.00 0.00 45.00 1.75
2341 3970 0.246635 ACCGCAACGCAGTCTAATCT 59.753 50.000 0.00 0.00 45.00 2.40
2342 3971 0.924090 CCGCAACGCAGTCTAATCTC 59.076 55.000 0.00 0.00 45.00 2.75
2343 3972 1.469940 CCGCAACGCAGTCTAATCTCT 60.470 52.381 0.00 0.00 45.00 3.10
2344 3973 1.585668 CGCAACGCAGTCTAATCTCTG 59.414 52.381 0.00 0.00 45.00 3.35
2345 3974 2.611518 GCAACGCAGTCTAATCTCTGT 58.388 47.619 0.00 0.00 45.00 3.41
2346 3975 2.346847 GCAACGCAGTCTAATCTCTGTG 59.653 50.000 0.00 0.00 45.00 3.66
2347 3976 2.285827 ACGCAGTCTAATCTCTGTGC 57.714 50.000 5.78 0.00 43.33 4.57
2348 3977 1.821753 ACGCAGTCTAATCTCTGTGCT 59.178 47.619 5.78 0.00 43.33 4.40
2349 3978 2.232452 ACGCAGTCTAATCTCTGTGCTT 59.768 45.455 5.78 0.00 43.33 3.91
2350 3979 3.444034 ACGCAGTCTAATCTCTGTGCTTA 59.556 43.478 5.78 0.00 43.33 3.09
2351 3980 4.041049 CGCAGTCTAATCTCTGTGCTTAG 58.959 47.826 0.00 0.00 35.84 2.18
2352 3981 4.201960 CGCAGTCTAATCTCTGTGCTTAGA 60.202 45.833 0.40 0.40 35.84 2.10
2353 3982 5.280945 GCAGTCTAATCTCTGTGCTTAGAG 58.719 45.833 10.42 10.42 44.42 2.43
2354 3983 5.280945 CAGTCTAATCTCTGTGCTTAGAGC 58.719 45.833 11.49 0.00 43.09 4.09
2355 3984 8.558395 GCAGTCTAATCTCTGTGCTTAGAGCA 62.558 46.154 11.49 0.00 43.09 4.26
2366 3995 3.075866 GCTTAGAGCATGCCATTTGTC 57.924 47.619 15.66 3.93 41.89 3.18
2367 3996 2.540361 GCTTAGAGCATGCCATTTGTCG 60.540 50.000 15.66 0.00 41.89 4.35
2368 3997 1.016627 TAGAGCATGCCATTTGTCGC 58.983 50.000 15.66 0.00 0.00 5.19
2369 3998 1.226773 GAGCATGCCATTTGTCGCC 60.227 57.895 15.66 0.00 0.00 5.54
2370 3999 2.580326 GCATGCCATTTGTCGCCG 60.580 61.111 6.36 0.00 0.00 6.46
2371 4000 2.580326 CATGCCATTTGTCGCCGC 60.580 61.111 0.00 0.00 0.00 6.53
2372 4001 3.061231 ATGCCATTTGTCGCCGCA 61.061 55.556 0.00 0.00 0.00 5.69
2373 4002 3.055080 ATGCCATTTGTCGCCGCAG 62.055 57.895 0.00 0.00 32.06 5.18
2375 4004 3.736100 CCATTTGTCGCCGCAGCA 61.736 61.111 0.00 0.00 39.83 4.41
2376 4005 2.202388 CATTTGTCGCCGCAGCAG 60.202 61.111 0.00 0.00 39.83 4.24
2377 4006 3.434319 ATTTGTCGCCGCAGCAGG 61.434 61.111 0.00 0.00 39.83 4.85
2397 4026 3.590574 GTCTGGGCCTGGGGGTTT 61.591 66.667 10.79 0.00 34.45 3.27
2398 4027 2.785389 TCTGGGCCTGGGGGTTTT 60.785 61.111 10.79 0.00 34.45 2.43
2399 4028 1.466386 TCTGGGCCTGGGGGTTTTA 60.466 57.895 10.79 0.00 34.45 1.52
2400 4029 1.000359 CTGGGCCTGGGGGTTTTAG 60.000 63.158 4.53 0.00 34.45 1.85
2401 4030 1.466386 TGGGCCTGGGGGTTTTAGA 60.466 57.895 4.53 0.00 34.45 2.10
2402 4031 1.000019 GGGCCTGGGGGTTTTAGAC 60.000 63.158 0.84 0.00 34.45 2.59
2403 4032 1.506907 GGGCCTGGGGGTTTTAGACT 61.507 60.000 0.84 0.00 34.45 3.24
2404 4033 0.408309 GGCCTGGGGGTTTTAGACTT 59.592 55.000 0.00 0.00 34.45 3.01
2405 4034 1.203137 GGCCTGGGGGTTTTAGACTTT 60.203 52.381 0.00 0.00 34.45 2.66
2406 4035 2.605257 GCCTGGGGGTTTTAGACTTTT 58.395 47.619 0.00 0.00 34.45 2.27
2407 4036 3.500836 GGCCTGGGGGTTTTAGACTTTTA 60.501 47.826 0.00 0.00 34.45 1.52
2408 4037 4.154176 GCCTGGGGGTTTTAGACTTTTAA 58.846 43.478 0.00 0.00 34.45 1.52
2409 4038 4.021719 GCCTGGGGGTTTTAGACTTTTAAC 60.022 45.833 0.00 0.00 34.45 2.01
2410 4039 4.525487 CCTGGGGGTTTTAGACTTTTAACC 59.475 45.833 0.00 0.00 39.41 2.85
2411 4040 5.391256 CTGGGGGTTTTAGACTTTTAACCT 58.609 41.667 0.00 0.00 39.90 3.50
2412 4041 6.467629 CCTGGGGGTTTTAGACTTTTAACCTA 60.468 42.308 0.00 0.00 39.90 3.08
2413 4042 6.545567 TGGGGGTTTTAGACTTTTAACCTAG 58.454 40.000 0.00 0.00 39.90 3.02
2414 4043 5.416952 GGGGGTTTTAGACTTTTAACCTAGC 59.583 44.000 0.00 0.00 39.90 3.42
2415 4044 6.005823 GGGGTTTTAGACTTTTAACCTAGCA 58.994 40.000 0.00 0.00 39.90 3.49
2416 4045 6.150641 GGGGTTTTAGACTTTTAACCTAGCAG 59.849 42.308 0.00 0.00 39.90 4.24
2417 4046 6.938596 GGGTTTTAGACTTTTAACCTAGCAGA 59.061 38.462 0.00 0.00 39.90 4.26
2418 4047 7.446319 GGGTTTTAGACTTTTAACCTAGCAGAA 59.554 37.037 0.00 0.00 39.90 3.02
2419 4048 8.504815 GGTTTTAGACTTTTAACCTAGCAGAAG 58.495 37.037 0.00 0.00 37.61 2.85
2420 4049 8.504815 GTTTTAGACTTTTAACCTAGCAGAAGG 58.495 37.037 0.00 0.00 42.82 3.46
2432 4061 6.382869 CCTAGCAGAAGGTTGGAAATAATG 57.617 41.667 0.00 0.00 39.98 1.90
2433 4062 5.888161 CCTAGCAGAAGGTTGGAAATAATGT 59.112 40.000 0.00 0.00 39.98 2.71
2434 4063 7.054124 CCTAGCAGAAGGTTGGAAATAATGTA 58.946 38.462 0.00 0.00 39.98 2.29
2435 4064 7.227512 CCTAGCAGAAGGTTGGAAATAATGTAG 59.772 40.741 0.00 0.00 39.98 2.74
2436 4065 6.721318 AGCAGAAGGTTGGAAATAATGTAGA 58.279 36.000 0.00 0.00 0.00 2.59
2437 4066 6.599638 AGCAGAAGGTTGGAAATAATGTAGAC 59.400 38.462 0.00 0.00 0.00 2.59
2438 4067 6.456988 GCAGAAGGTTGGAAATAATGTAGACG 60.457 42.308 0.00 0.00 0.00 4.18
2439 4068 6.037172 CAGAAGGTTGGAAATAATGTAGACGG 59.963 42.308 0.00 0.00 0.00 4.79
2440 4069 4.196971 AGGTTGGAAATAATGTAGACGGC 58.803 43.478 0.00 0.00 0.00 5.68
2441 4070 3.001939 GGTTGGAAATAATGTAGACGGCG 59.998 47.826 4.80 4.80 0.00 6.46
2442 4071 2.828877 TGGAAATAATGTAGACGGCGG 58.171 47.619 13.24 0.00 0.00 6.13
2443 4072 2.140717 GGAAATAATGTAGACGGCGGG 58.859 52.381 13.24 0.00 0.00 6.13
2444 4073 2.484241 GGAAATAATGTAGACGGCGGGT 60.484 50.000 13.24 0.00 0.00 5.28
2445 4074 2.234300 AATAATGTAGACGGCGGGTG 57.766 50.000 13.24 0.00 0.00 4.61
2446 4075 0.249741 ATAATGTAGACGGCGGGTGC 60.250 55.000 13.24 1.34 41.71 5.01
2457 4086 4.160635 CGGGTGCCGCGTCATTTC 62.161 66.667 4.92 0.00 41.17 2.17
2458 4087 4.160635 GGGTGCCGCGTCATTTCG 62.161 66.667 4.92 0.00 0.00 3.46
2478 4107 1.588404 GGCACGTGATGTTATGTCTCG 59.412 52.381 22.23 0.00 38.23 4.04
2479 4108 1.588404 GCACGTGATGTTATGTCTCGG 59.412 52.381 22.23 0.00 37.03 4.63
2480 4109 2.193447 CACGTGATGTTATGTCTCGGG 58.807 52.381 10.90 0.00 37.03 5.14
2481 4110 1.822990 ACGTGATGTTATGTCTCGGGT 59.177 47.619 0.00 0.00 37.03 5.28
2482 4111 2.193447 CGTGATGTTATGTCTCGGGTG 58.807 52.381 0.00 0.00 0.00 4.61
2483 4112 1.933853 GTGATGTTATGTCTCGGGTGC 59.066 52.381 0.00 0.00 0.00 5.01
2484 4113 1.552792 TGATGTTATGTCTCGGGTGCA 59.447 47.619 0.00 0.00 0.00 4.57
2485 4114 2.205074 GATGTTATGTCTCGGGTGCAG 58.795 52.381 0.00 0.00 0.00 4.41
2486 4115 0.249120 TGTTATGTCTCGGGTGCAGG 59.751 55.000 0.00 0.00 0.00 4.85
2487 4116 0.462047 GTTATGTCTCGGGTGCAGGG 60.462 60.000 0.00 0.00 0.00 4.45
2488 4117 2.252072 TTATGTCTCGGGTGCAGGGC 62.252 60.000 0.00 0.00 0.00 5.19
2509 4138 4.681978 GGCGTGAGGGCGAGTGTT 62.682 66.667 0.00 0.00 0.00 3.32
2510 4139 3.414700 GCGTGAGGGCGAGTGTTG 61.415 66.667 0.00 0.00 0.00 3.33
2511 4140 2.738521 CGTGAGGGCGAGTGTTGG 60.739 66.667 0.00 0.00 0.00 3.77
2512 4141 2.358737 GTGAGGGCGAGTGTTGGG 60.359 66.667 0.00 0.00 0.00 4.12
2513 4142 2.847234 TGAGGGCGAGTGTTGGGT 60.847 61.111 0.00 0.00 0.00 4.51
2514 4143 1.534476 TGAGGGCGAGTGTTGGGTA 60.534 57.895 0.00 0.00 0.00 3.69
2515 4144 0.907704 TGAGGGCGAGTGTTGGGTAT 60.908 55.000 0.00 0.00 0.00 2.73
2516 4145 0.462047 GAGGGCGAGTGTTGGGTATG 60.462 60.000 0.00 0.00 0.00 2.39
2517 4146 0.907704 AGGGCGAGTGTTGGGTATGA 60.908 55.000 0.00 0.00 0.00 2.15
2518 4147 0.180406 GGGCGAGTGTTGGGTATGAT 59.820 55.000 0.00 0.00 0.00 2.45
2519 4148 1.408266 GGGCGAGTGTTGGGTATGATT 60.408 52.381 0.00 0.00 0.00 2.57
2520 4149 1.670811 GGCGAGTGTTGGGTATGATTG 59.329 52.381 0.00 0.00 0.00 2.67
2521 4150 2.627945 GCGAGTGTTGGGTATGATTGA 58.372 47.619 0.00 0.00 0.00 2.57
2522 4151 2.351726 GCGAGTGTTGGGTATGATTGAC 59.648 50.000 0.00 0.00 0.00 3.18
2523 4152 2.936498 CGAGTGTTGGGTATGATTGACC 59.064 50.000 0.00 0.00 36.12 4.02
2532 4161 3.606687 GGTATGATTGACCCGTTGAACT 58.393 45.455 0.00 0.00 0.00 3.01
2533 4162 3.374058 GGTATGATTGACCCGTTGAACTG 59.626 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 205 4.863152 AAAACTTGTTGAAGCAATGCAC 57.137 36.364 8.35 1.42 31.68 4.57
51 208 9.424659 GAACAAATAAAACTTGTTGAAGCAATG 57.575 29.630 5.72 0.00 44.85 2.82
64 221 3.634910 AGCACCGTGGAACAAATAAAACT 59.365 39.130 0.00 0.00 44.16 2.66
74 231 3.181500 GGAATTAATCAGCACCGTGGAAC 60.181 47.826 0.00 0.00 0.00 3.62
86 243 7.658167 TGACGTTGTTTGACTAGGAATTAATCA 59.342 33.333 0.00 0.00 0.00 2.57
105 262 8.964150 TCAATATACGACAGATTATTGACGTTG 58.036 33.333 8.55 2.56 44.49 4.10
117 275 8.560374 CACTCTTCACTATCAATATACGACAGA 58.440 37.037 0.00 0.00 0.00 3.41
130 288 8.920665 GTGAATATATGCACACTCTTCACTATC 58.079 37.037 17.68 0.00 38.48 2.08
134 292 6.908870 TGTGAATATATGCACACTCTTCAC 57.091 37.500 20.79 11.61 39.86 3.18
163 321 1.863267 TTTTGGCCGTGCTGATTTTG 58.137 45.000 0.00 0.00 0.00 2.44
231 390 2.595009 CTAAGGGACCTCGCAAGCCC 62.595 65.000 0.00 0.00 41.00 5.19
236 395 2.038975 AGCCTAAGGGACCTCGCA 59.961 61.111 0.00 0.00 33.58 5.10
387 1896 0.972983 CTCGGTGACATCCCCAGAGT 60.973 60.000 0.00 0.00 0.00 3.24
396 1905 2.579201 CTTCGGCCTCGGTGACAT 59.421 61.111 0.00 0.00 36.95 3.06
412 1921 1.077993 AGTTGAGTCCTAGAGGCACCT 59.922 52.381 0.00 0.00 34.44 4.00
431 1940 3.326297 AGAAAGAAGGTCACCTCCTTGAG 59.674 47.826 0.00 0.00 46.38 3.02
432 1941 3.318313 AGAAAGAAGGTCACCTCCTTGA 58.682 45.455 0.00 0.00 46.38 3.02
433 1942 3.778954 AGAAAGAAGGTCACCTCCTTG 57.221 47.619 0.00 0.00 46.38 3.61
435 1944 3.445987 CCTAGAAAGAAGGTCACCTCCT 58.554 50.000 0.00 0.00 39.84 3.69
436 1945 2.093394 GCCTAGAAAGAAGGTCACCTCC 60.093 54.545 0.00 0.00 36.43 4.30
437 1946 2.835156 AGCCTAGAAAGAAGGTCACCTC 59.165 50.000 0.00 0.00 36.43 3.85
438 1947 2.909217 AGCCTAGAAAGAAGGTCACCT 58.091 47.619 0.00 0.00 36.43 4.00
439 1948 3.704800 AAGCCTAGAAAGAAGGTCACC 57.295 47.619 0.00 0.00 36.43 4.02
475 1988 5.701290 CAGTTTCCGGACAGAGAAATAAACT 59.299 40.000 1.83 4.09 36.61 2.66
476 1989 5.699458 TCAGTTTCCGGACAGAGAAATAAAC 59.301 40.000 1.83 1.31 34.69 2.01
477 1990 5.860611 TCAGTTTCCGGACAGAGAAATAAA 58.139 37.500 1.83 0.00 34.69 1.40
478 1991 5.477607 TCAGTTTCCGGACAGAGAAATAA 57.522 39.130 1.83 0.00 34.69 1.40
479 1992 4.620803 GCTCAGTTTCCGGACAGAGAAATA 60.621 45.833 16.84 0.00 35.80 1.40
480 1993 3.866449 GCTCAGTTTCCGGACAGAGAAAT 60.866 47.826 16.84 0.30 35.80 2.17
481 1994 2.548067 GCTCAGTTTCCGGACAGAGAAA 60.548 50.000 16.84 0.15 35.80 2.52
482 1995 1.000955 GCTCAGTTTCCGGACAGAGAA 59.999 52.381 16.84 0.87 35.80 2.87
483 1996 0.603569 GCTCAGTTTCCGGACAGAGA 59.396 55.000 16.84 7.57 35.80 3.10
492 2014 2.038557 TGGAAGTGTAGGCTCAGTTTCC 59.961 50.000 11.62 11.62 35.06 3.13
536 2058 4.878971 CCCATACCACGTGAATACAAATCA 59.121 41.667 19.30 0.00 0.00 2.57
607 2139 3.767673 AGCAAGCAAACCATTCATCAGAT 59.232 39.130 0.00 0.00 0.00 2.90
608 2140 3.159472 AGCAAGCAAACCATTCATCAGA 58.841 40.909 0.00 0.00 0.00 3.27
633 2165 1.745827 GCCCACGGATTTAGCTAAGCA 60.746 52.381 6.24 0.00 0.00 3.91
666 2198 5.174037 TCAAACACCTTCCCTACATAAGG 57.826 43.478 0.00 0.00 46.44 2.69
677 2209 4.762251 AGAGGCACTTTATCAAACACCTTC 59.238 41.667 0.00 0.00 41.55 3.46
714 2246 2.223688 TGAACAACAAAGCACCCATTCG 60.224 45.455 0.00 0.00 0.00 3.34
734 2266 7.687941 AAAGTAATTAACTGGATGTCCTGTG 57.312 36.000 11.66 0.21 45.74 3.66
767 2299 5.065090 GCAGGAAATATTTTGGAAACCATGC 59.935 40.000 1.43 3.70 31.53 4.06
782 2314 3.871701 TGCGATGTGGCAGGAAATA 57.128 47.368 0.00 0.00 38.17 1.40
805 2337 4.261572 GCTGCAAATGGTAAGACTGAACAA 60.262 41.667 0.00 0.00 0.00 2.83
806 2338 3.253188 GCTGCAAATGGTAAGACTGAACA 59.747 43.478 0.00 0.00 0.00 3.18
813 2345 3.888323 TGAAGTTGCTGCAAATGGTAAGA 59.112 39.130 17.80 0.00 0.00 2.10
901 2433 6.889198 AGAGCATAGCTTGTTATACCTTTCA 58.111 36.000 0.00 0.00 39.88 2.69
907 2439 9.535878 AAGAAGTAAGAGCATAGCTTGTTATAC 57.464 33.333 0.00 0.00 39.88 1.47
909 2441 9.535878 GTAAGAAGTAAGAGCATAGCTTGTTAT 57.464 33.333 0.00 0.00 39.88 1.89
915 2447 5.362430 AGCTGTAAGAAGTAAGAGCATAGCT 59.638 40.000 0.00 0.00 37.77 3.32
924 2456 3.681897 CCTGCACAGCTGTAAGAAGTAAG 59.318 47.826 21.20 4.76 34.07 2.34
925 2457 3.071023 ACCTGCACAGCTGTAAGAAGTAA 59.929 43.478 21.20 0.00 34.07 2.24
926 2458 2.632996 ACCTGCACAGCTGTAAGAAGTA 59.367 45.455 21.20 5.35 34.07 2.24
927 2459 1.417890 ACCTGCACAGCTGTAAGAAGT 59.582 47.619 21.20 10.76 34.07 3.01
934 2466 2.862541 TCAATTAACCTGCACAGCTGT 58.137 42.857 15.25 15.25 0.00 4.40
953 2485 2.164624 CTCCTTATGGGGATCGACGATC 59.835 54.545 26.21 26.21 35.23 3.69
1119 2651 3.428589 GGATGCACCATTTCTCTTTCAGC 60.429 47.826 0.00 0.00 38.79 4.26
1164 2696 4.101448 CTGACCCAGGAAGCCCCG 62.101 72.222 0.00 0.00 40.87 5.73
1233 2765 0.321671 TGCTGCTGTTAGGGTCAGAC 59.678 55.000 0.00 0.00 35.20 3.51
1251 2783 0.178935 TTTTCCCCTCCTTGGCCTTG 60.179 55.000 3.32 0.00 0.00 3.61
1252 2784 0.178932 GTTTTCCCCTCCTTGGCCTT 60.179 55.000 3.32 0.00 0.00 4.35
1253 2785 1.074296 AGTTTTCCCCTCCTTGGCCT 61.074 55.000 3.32 0.00 0.00 5.19
1254 2786 0.702316 TAGTTTTCCCCTCCTTGGCC 59.298 55.000 0.00 0.00 0.00 5.36
1255 2787 1.835494 GTAGTTTTCCCCTCCTTGGC 58.165 55.000 0.00 0.00 0.00 4.52
1275 2810 0.527385 CAAGCAGACTAGGCTCGCTC 60.527 60.000 18.95 0.25 41.66 5.03
1278 2813 0.102120 CCTCAAGCAGACTAGGCTCG 59.898 60.000 0.00 0.00 41.66 5.03
1371 2906 0.098376 CCGCACTCGTGTAGGTAGAC 59.902 60.000 0.00 0.00 0.00 2.59
1446 2981 0.329596 GGTGATCCTTCCCAGCAACT 59.670 55.000 0.00 0.00 0.00 3.16
1571 3169 4.295870 TGTATATAAACGAGAAGCTGCGG 58.704 43.478 8.46 0.00 0.00 5.69
1592 3190 5.902681 TCTACCCGACTTGTGATAAGAATG 58.097 41.667 0.00 0.00 0.00 2.67
1594 3192 5.244402 TGTTCTACCCGACTTGTGATAAGAA 59.756 40.000 0.00 0.00 0.00 2.52
1603 3201 3.057734 GTTGTCTGTTCTACCCGACTTG 58.942 50.000 0.00 0.00 0.00 3.16
1621 3219 0.661187 AAACGAGCAGCGCATTGTTG 60.661 50.000 11.47 0.00 46.04 3.33
1625 3223 5.639506 AGAATATATAAACGAGCAGCGCATT 59.360 36.000 11.47 0.00 46.04 3.56
1641 3239 8.820831 CCAGGACAAGGTCAGATAAGAATATAT 58.179 37.037 0.00 0.00 33.68 0.86
1642 3240 7.235606 CCCAGGACAAGGTCAGATAAGAATATA 59.764 40.741 0.00 0.00 33.68 0.86
1643 3241 6.043706 CCCAGGACAAGGTCAGATAAGAATAT 59.956 42.308 0.00 0.00 33.68 1.28
1644 3242 5.366768 CCCAGGACAAGGTCAGATAAGAATA 59.633 44.000 0.00 0.00 33.68 1.75
1646 3244 3.519510 CCCAGGACAAGGTCAGATAAGAA 59.480 47.826 0.00 0.00 33.68 2.52
1648 3246 2.840651 ACCCAGGACAAGGTCAGATAAG 59.159 50.000 0.00 0.00 33.68 1.73
1649 3247 2.915869 ACCCAGGACAAGGTCAGATAA 58.084 47.619 0.00 0.00 33.68 1.75
1650 3248 2.642171 ACCCAGGACAAGGTCAGATA 57.358 50.000 0.00 0.00 33.68 1.98
1652 3250 2.409064 TAACCCAGGACAAGGTCAGA 57.591 50.000 0.00 0.00 34.45 3.27
1653 3251 2.305927 ACATAACCCAGGACAAGGTCAG 59.694 50.000 0.00 0.00 34.45 3.51
1654 3252 2.039746 CACATAACCCAGGACAAGGTCA 59.960 50.000 0.00 0.00 34.45 4.02
1655 3253 2.304761 TCACATAACCCAGGACAAGGTC 59.695 50.000 0.00 0.00 34.45 3.85
1656 3254 2.039879 GTCACATAACCCAGGACAAGGT 59.960 50.000 0.00 0.00 38.27 3.50
1658 3256 2.305927 AGGTCACATAACCCAGGACAAG 59.694 50.000 0.00 0.00 40.42 3.16
1660 3258 2.038863 AGGTCACATAACCCAGGACA 57.961 50.000 0.00 0.00 40.42 4.02
1663 3261 3.261981 GTGTAGGTCACATAACCCAGG 57.738 52.381 0.00 0.00 45.51 4.45
1716 3345 1.280133 TGGAGAAGGGAATGACTGCAG 59.720 52.381 13.48 13.48 0.00 4.41
1757 3386 0.607489 GCAAGCACACAGTCCTGGAT 60.607 55.000 0.00 0.00 34.19 3.41
1760 3389 0.820891 AAGGCAAGCACACAGTCCTG 60.821 55.000 0.00 0.00 0.00 3.86
1764 3393 0.457035 CAACAAGGCAAGCACACAGT 59.543 50.000 0.00 0.00 0.00 3.55
1783 3412 4.859245 GCCTTTGTTTCTGTTATTGCTAGC 59.141 41.667 8.10 8.10 0.00 3.42
1784 3413 5.402398 GGCCTTTGTTTCTGTTATTGCTAG 58.598 41.667 0.00 0.00 0.00 3.42
1785 3414 4.219725 GGGCCTTTGTTTCTGTTATTGCTA 59.780 41.667 0.84 0.00 0.00 3.49
1786 3415 3.006859 GGGCCTTTGTTTCTGTTATTGCT 59.993 43.478 0.84 0.00 0.00 3.91
1787 3416 3.244044 TGGGCCTTTGTTTCTGTTATTGC 60.244 43.478 4.53 0.00 0.00 3.56
1788 3417 4.599047 TGGGCCTTTGTTTCTGTTATTG 57.401 40.909 4.53 0.00 0.00 1.90
1789 3418 4.222810 GGATGGGCCTTTGTTTCTGTTATT 59.777 41.667 4.53 0.00 0.00 1.40
1790 3419 3.769300 GGATGGGCCTTTGTTTCTGTTAT 59.231 43.478 4.53 0.00 0.00 1.89
1791 3420 3.161866 GGATGGGCCTTTGTTTCTGTTA 58.838 45.455 4.53 0.00 0.00 2.41
1825 3454 2.535534 CGCACATTGCAGAGTTACATCG 60.536 50.000 0.00 0.00 45.36 3.84
1830 3459 1.305219 GGGCGCACATTGCAGAGTTA 61.305 55.000 10.83 0.00 45.36 2.24
1831 3460 2.629656 GGGCGCACATTGCAGAGTT 61.630 57.895 10.83 0.00 45.36 3.01
1851 3480 2.322161 ACAAAGTACCAACGACGATCG 58.678 47.619 14.88 14.88 46.93 3.69
1869 3498 2.294074 GTGCTTGTCACCCTACAAACA 58.706 47.619 0.00 0.00 38.81 2.83
1870 3499 2.290641 CTGTGCTTGTCACCCTACAAAC 59.709 50.000 0.00 0.00 45.03 2.93
1871 3500 2.092646 ACTGTGCTTGTCACCCTACAAA 60.093 45.455 0.00 0.00 45.03 2.83
1872 3501 1.488812 ACTGTGCTTGTCACCCTACAA 59.511 47.619 0.00 0.00 45.03 2.41
1980 3609 0.036732 CACCTAACTCAAGGCCAGCA 59.963 55.000 5.01 0.00 40.62 4.41
2098 3727 3.135994 CTGTGTTTGGTACCCTACACAC 58.864 50.000 30.51 24.86 41.22 3.82
2099 3728 2.773087 ACTGTGTTTGGTACCCTACACA 59.227 45.455 31.26 31.26 42.57 3.72
2100 3729 3.480505 ACTGTGTTTGGTACCCTACAC 57.519 47.619 27.37 27.37 38.90 2.90
2131 3760 6.315642 CAGGCAGACATATAATAAGCCATGAG 59.684 42.308 0.00 0.00 42.90 2.90
2132 3761 6.175471 CAGGCAGACATATAATAAGCCATGA 58.825 40.000 0.00 0.00 42.90 3.07
2176 3805 9.360901 CATGTACTGCTGGATATATAGATAGGT 57.639 37.037 0.00 0.00 0.00 3.08
2177 3806 9.360901 ACATGTACTGCTGGATATATAGATAGG 57.639 37.037 0.00 0.00 0.00 2.57
2191 3820 6.712549 CATCAATCAGTAACATGTACTGCTG 58.287 40.000 21.17 15.89 43.30 4.41
2201 3830 3.354948 AGCCTGCATCAATCAGTAACA 57.645 42.857 0.00 0.00 0.00 2.41
2216 3845 0.320771 AGCAACCACGACTAAGCCTG 60.321 55.000 0.00 0.00 0.00 4.85
2241 3870 0.381089 CGAGCTGGTTAGACCTACCG 59.619 60.000 0.00 0.00 39.58 4.02
2254 3883 0.179150 GGCACTGTAGAGACGAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
2266 3895 4.555709 TCGTTTGCCGGGCACTGT 62.556 61.111 23.78 0.00 38.71 3.55
2276 3905 1.008538 CCAGTGGCTTGTCGTTTGC 60.009 57.895 0.00 0.00 0.00 3.68
2306 3935 0.863144 CGGTTGTGGTACAGTTTCGG 59.137 55.000 0.00 0.00 41.80 4.30
2328 3957 1.821753 AGCACAGAGATTAGACTGCGT 59.178 47.619 0.00 0.00 37.61 5.24
2331 3960 5.280945 GCTCTAAGCACAGAGATTAGACTG 58.719 45.833 16.42 0.00 46.98 3.51
2346 3975 2.540361 CGACAAATGGCATGCTCTAAGC 60.540 50.000 18.92 0.00 42.82 3.09
2347 3976 2.540361 GCGACAAATGGCATGCTCTAAG 60.540 50.000 18.92 7.97 0.00 2.18
2348 3977 1.401552 GCGACAAATGGCATGCTCTAA 59.598 47.619 18.92 1.32 0.00 2.10
2349 3978 1.016627 GCGACAAATGGCATGCTCTA 58.983 50.000 18.92 4.93 0.00 2.43
2350 3979 1.660560 GGCGACAAATGGCATGCTCT 61.661 55.000 18.92 1.78 0.00 4.09
2351 3980 1.226773 GGCGACAAATGGCATGCTC 60.227 57.895 18.92 8.46 0.00 4.26
2352 3981 2.887360 GGCGACAAATGGCATGCT 59.113 55.556 18.92 0.00 0.00 3.79
2353 3982 2.580326 CGGCGACAAATGGCATGC 60.580 61.111 9.90 9.90 0.00 4.06
2354 3983 2.580326 GCGGCGACAAATGGCATG 60.580 61.111 12.98 0.00 0.00 4.06
2355 3984 3.055080 CTGCGGCGACAAATGGCAT 62.055 57.895 12.98 0.00 32.55 4.40
2356 3985 3.736100 CTGCGGCGACAAATGGCA 61.736 61.111 12.98 0.00 0.00 4.92
2358 3987 3.672255 CTGCTGCGGCGACAAATGG 62.672 63.158 12.98 0.00 42.25 3.16
2359 3988 2.202388 CTGCTGCGGCGACAAATG 60.202 61.111 12.98 0.00 42.25 2.32
2360 3989 3.434319 CCTGCTGCGGCGACAAAT 61.434 61.111 12.98 0.00 42.25 2.32
2380 4009 1.795951 TAAAACCCCCAGGCCCAGAC 61.796 60.000 0.00 0.00 36.11 3.51
2381 4010 1.466386 TAAAACCCCCAGGCCCAGA 60.466 57.895 0.00 0.00 36.11 3.86
2382 4011 1.000359 CTAAAACCCCCAGGCCCAG 60.000 63.158 0.00 0.00 36.11 4.45
2383 4012 1.466386 TCTAAAACCCCCAGGCCCA 60.466 57.895 0.00 0.00 36.11 5.36
2384 4013 1.000019 GTCTAAAACCCCCAGGCCC 60.000 63.158 0.00 0.00 36.11 5.80
2385 4014 0.408309 AAGTCTAAAACCCCCAGGCC 59.592 55.000 0.00 0.00 36.11 5.19
2386 4015 2.304221 AAAGTCTAAAACCCCCAGGC 57.696 50.000 0.00 0.00 36.11 4.85
2387 4016 4.525487 GGTTAAAAGTCTAAAACCCCCAGG 59.475 45.833 0.00 0.00 36.24 4.45
2388 4017 5.391256 AGGTTAAAAGTCTAAAACCCCCAG 58.609 41.667 7.11 0.00 41.93 4.45
2389 4018 5.406570 AGGTTAAAAGTCTAAAACCCCCA 57.593 39.130 7.11 0.00 41.93 4.96
2390 4019 5.416952 GCTAGGTTAAAAGTCTAAAACCCCC 59.583 44.000 7.11 0.00 41.93 5.40
2391 4020 6.005823 TGCTAGGTTAAAAGTCTAAAACCCC 58.994 40.000 7.11 0.00 41.93 4.95
2392 4021 6.938596 TCTGCTAGGTTAAAAGTCTAAAACCC 59.061 38.462 7.11 0.00 41.93 4.11
2393 4022 7.974482 TCTGCTAGGTTAAAAGTCTAAAACC 57.026 36.000 0.00 0.00 41.41 3.27
2394 4023 8.504815 CCTTCTGCTAGGTTAAAAGTCTAAAAC 58.495 37.037 0.00 0.00 0.00 2.43
2395 4024 8.215736 ACCTTCTGCTAGGTTAAAAGTCTAAAA 58.784 33.333 0.00 0.00 46.39 1.52
2396 4025 7.742767 ACCTTCTGCTAGGTTAAAAGTCTAAA 58.257 34.615 0.00 0.00 46.39 1.85
2397 4026 7.312415 ACCTTCTGCTAGGTTAAAAGTCTAA 57.688 36.000 0.00 0.00 46.39 2.10
2398 4027 6.930068 ACCTTCTGCTAGGTTAAAAGTCTA 57.070 37.500 0.00 0.00 46.39 2.59
2399 4028 5.827326 ACCTTCTGCTAGGTTAAAAGTCT 57.173 39.130 0.00 0.00 46.39 3.24
2409 4038 5.888161 ACATTATTTCCAACCTTCTGCTAGG 59.112 40.000 0.00 0.00 41.31 3.02
2410 4039 7.987458 TCTACATTATTTCCAACCTTCTGCTAG 59.013 37.037 0.00 0.00 0.00 3.42
2411 4040 7.769044 GTCTACATTATTTCCAACCTTCTGCTA 59.231 37.037 0.00 0.00 0.00 3.49
2412 4041 6.599638 GTCTACATTATTTCCAACCTTCTGCT 59.400 38.462 0.00 0.00 0.00 4.24
2413 4042 6.456988 CGTCTACATTATTTCCAACCTTCTGC 60.457 42.308 0.00 0.00 0.00 4.26
2414 4043 6.037172 CCGTCTACATTATTTCCAACCTTCTG 59.963 42.308 0.00 0.00 0.00 3.02
2415 4044 6.113411 CCGTCTACATTATTTCCAACCTTCT 58.887 40.000 0.00 0.00 0.00 2.85
2416 4045 5.220796 GCCGTCTACATTATTTCCAACCTTC 60.221 44.000 0.00 0.00 0.00 3.46
2417 4046 4.638865 GCCGTCTACATTATTTCCAACCTT 59.361 41.667 0.00 0.00 0.00 3.50
2418 4047 4.196971 GCCGTCTACATTATTTCCAACCT 58.803 43.478 0.00 0.00 0.00 3.50
2419 4048 3.001939 CGCCGTCTACATTATTTCCAACC 59.998 47.826 0.00 0.00 0.00 3.77
2420 4049 3.001939 CCGCCGTCTACATTATTTCCAAC 59.998 47.826 0.00 0.00 0.00 3.77
2421 4050 3.199677 CCGCCGTCTACATTATTTCCAA 58.800 45.455 0.00 0.00 0.00 3.53
2422 4051 2.484065 CCCGCCGTCTACATTATTTCCA 60.484 50.000 0.00 0.00 0.00 3.53
2423 4052 2.140717 CCCGCCGTCTACATTATTTCC 58.859 52.381 0.00 0.00 0.00 3.13
2424 4053 2.542595 CACCCGCCGTCTACATTATTTC 59.457 50.000 0.00 0.00 0.00 2.17
2425 4054 2.557317 CACCCGCCGTCTACATTATTT 58.443 47.619 0.00 0.00 0.00 1.40
2426 4055 1.808891 GCACCCGCCGTCTACATTATT 60.809 52.381 0.00 0.00 0.00 1.40
2427 4056 0.249741 GCACCCGCCGTCTACATTAT 60.250 55.000 0.00 0.00 0.00 1.28
2428 4057 1.142314 GCACCCGCCGTCTACATTA 59.858 57.895 0.00 0.00 0.00 1.90
2429 4058 2.125269 GCACCCGCCGTCTACATT 60.125 61.111 0.00 0.00 0.00 2.71
2441 4070 4.160635 CGAAATGACGCGGCACCC 62.161 66.667 21.63 8.64 0.00 4.61
2442 4071 4.160635 CCGAAATGACGCGGCACC 62.161 66.667 21.63 9.08 41.17 5.01
2447 4076 3.773630 ACGTGCCGAAATGACGCG 61.774 61.111 3.53 3.53 42.64 6.01
2448 4077 1.966493 ATCACGTGCCGAAATGACGC 61.966 55.000 11.67 0.00 36.56 5.19
2449 4078 0.247262 CATCACGTGCCGAAATGACG 60.247 55.000 11.67 0.00 39.03 4.35
2450 4079 0.796312 ACATCACGTGCCGAAATGAC 59.204 50.000 17.99 0.00 0.00 3.06
2451 4080 1.518325 AACATCACGTGCCGAAATGA 58.482 45.000 17.99 0.00 0.00 2.57
2452 4081 3.181511 ACATAACATCACGTGCCGAAATG 60.182 43.478 11.67 11.53 0.00 2.32
2453 4082 3.006940 ACATAACATCACGTGCCGAAAT 58.993 40.909 11.67 0.00 0.00 2.17
2454 4083 2.413796 GACATAACATCACGTGCCGAAA 59.586 45.455 11.67 0.00 0.00 3.46
2455 4084 1.996898 GACATAACATCACGTGCCGAA 59.003 47.619 11.67 0.00 0.00 4.30
2456 4085 1.203758 AGACATAACATCACGTGCCGA 59.796 47.619 11.67 0.00 0.00 5.54
2457 4086 1.588404 GAGACATAACATCACGTGCCG 59.412 52.381 11.67 6.58 0.00 5.69
2458 4087 1.588404 CGAGACATAACATCACGTGCC 59.412 52.381 11.67 0.00 0.00 5.01
2459 4088 1.588404 CCGAGACATAACATCACGTGC 59.412 52.381 11.67 0.00 0.00 5.34
2460 4089 2.193447 CCCGAGACATAACATCACGTG 58.807 52.381 9.94 9.94 0.00 4.49
2461 4090 1.822990 ACCCGAGACATAACATCACGT 59.177 47.619 0.00 0.00 0.00 4.49
2462 4091 2.193447 CACCCGAGACATAACATCACG 58.807 52.381 0.00 0.00 0.00 4.35
2463 4092 1.933853 GCACCCGAGACATAACATCAC 59.066 52.381 0.00 0.00 0.00 3.06
2464 4093 1.552792 TGCACCCGAGACATAACATCA 59.447 47.619 0.00 0.00 0.00 3.07
2465 4094 2.205074 CTGCACCCGAGACATAACATC 58.795 52.381 0.00 0.00 0.00 3.06
2466 4095 1.134401 CCTGCACCCGAGACATAACAT 60.134 52.381 0.00 0.00 0.00 2.71
2467 4096 0.249120 CCTGCACCCGAGACATAACA 59.751 55.000 0.00 0.00 0.00 2.41
2468 4097 0.462047 CCCTGCACCCGAGACATAAC 60.462 60.000 0.00 0.00 0.00 1.89
2469 4098 1.904771 CCCTGCACCCGAGACATAA 59.095 57.895 0.00 0.00 0.00 1.90
2470 4099 2.731571 GCCCTGCACCCGAGACATA 61.732 63.158 0.00 0.00 0.00 2.29
2471 4100 4.101448 GCCCTGCACCCGAGACAT 62.101 66.667 0.00 0.00 0.00 3.06
2492 4121 4.681978 AACACTCGCCCTCACGCC 62.682 66.667 0.00 0.00 0.00 5.68
2493 4122 3.414700 CAACACTCGCCCTCACGC 61.415 66.667 0.00 0.00 0.00 5.34
2494 4123 2.738521 CCAACACTCGCCCTCACG 60.739 66.667 0.00 0.00 0.00 4.35
2495 4124 1.823169 TACCCAACACTCGCCCTCAC 61.823 60.000 0.00 0.00 0.00 3.51
2496 4125 0.907704 ATACCCAACACTCGCCCTCA 60.908 55.000 0.00 0.00 0.00 3.86
2497 4126 0.462047 CATACCCAACACTCGCCCTC 60.462 60.000 0.00 0.00 0.00 4.30
2498 4127 0.907704 TCATACCCAACACTCGCCCT 60.908 55.000 0.00 0.00 0.00 5.19
2499 4128 0.180406 ATCATACCCAACACTCGCCC 59.820 55.000 0.00 0.00 0.00 6.13
2500 4129 1.670811 CAATCATACCCAACACTCGCC 59.329 52.381 0.00 0.00 0.00 5.54
2501 4130 2.351726 GTCAATCATACCCAACACTCGC 59.648 50.000 0.00 0.00 0.00 5.03
2502 4131 2.936498 GGTCAATCATACCCAACACTCG 59.064 50.000 0.00 0.00 0.00 4.18
2511 4140 3.374058 CAGTTCAACGGGTCAATCATACC 59.626 47.826 0.00 0.00 36.19 2.73
2512 4141 4.600012 CAGTTCAACGGGTCAATCATAC 57.400 45.455 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.