Multiple sequence alignment - TraesCS6D01G241100

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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 TraesCS6D01G241100 chr6D 100.000 6375 0 0 1 6375 343551942 343558316 0.000000e+00 11773.0
1 TraesCS6D01G241100 chr6D 86.364 132 13 4 4155 4285 68649955 68650082 8.620000e-29 139.0
2 TraesCS6D01G241100 chr6A 94.071 3626 118 31 748 4325 483895395 483898971 0.000000e+00 5415.0
3 TraesCS6D01G241100 chr6A 93.756 2002 57 26 4428 6375 483898969 483900956 0.000000e+00 2942.0
4 TraesCS6D01G241100 chr6A 97.321 112 3 0 4322 4433 499205118 499205007 2.350000e-44 191.0
5 TraesCS6D01G241100 chr6A 87.838 148 16 2 4307 4452 206322041 206321894 8.500000e-39 172.0
6 TraesCS6D01G241100 chr6B 91.738 2469 130 30 793 3201 518386530 518388984 0.000000e+00 3362.0
7 TraesCS6D01G241100 chr6B 94.037 1241 54 13 4611 5836 518390426 518391661 0.000000e+00 1864.0
8 TraesCS6D01G241100 chr6B 91.540 591 34 10 50 633 518381062 518381643 0.000000e+00 800.0
9 TraesCS6D01G241100 chr6B 91.328 369 22 6 3203 3564 518389068 518389433 4.440000e-136 496.0
10 TraesCS6D01G241100 chr6B 88.333 420 31 10 3563 3973 518389527 518389937 7.430000e-134 488.0
11 TraesCS6D01G241100 chr6B 96.269 268 10 0 6108 6375 518392044 518392311 2.110000e-119 440.0
12 TraesCS6D01G241100 chr6B 89.286 280 13 4 4028 4290 518389956 518390235 1.020000e-87 335.0
13 TraesCS6D01G241100 chr6B 90.476 147 7 5 4430 4573 518390286 518390428 3.030000e-43 187.0
14 TraesCS6D01G241100 chr6B 89.109 101 7 3 625 725 518384620 518384716 8.680000e-24 122.0
15 TraesCS6D01G241100 chr6B 93.750 48 3 0 1 48 518380991 518381038 8.870000e-09 73.1
16 TraesCS6D01G241100 chr7A 81.446 415 47 17 5299 5698 581045336 581044937 4.800000e-81 313.0
17 TraesCS6D01G241100 chr1D 98.276 116 2 0 4322 4437 69088103 69087988 3.010000e-48 204.0
18 TraesCS6D01G241100 chr5A 98.198 111 2 0 4321 4431 706934078 706933968 1.810000e-45 195.0
19 TraesCS6D01G241100 chr5A 94.355 124 5 2 4317 4439 55248083 55247961 8.440000e-44 189.0
20 TraesCS6D01G241100 chr3A 98.182 110 2 0 4320 4429 336604644 336604535 6.520000e-45 193.0
21 TraesCS6D01G241100 chr2A 96.522 115 4 0 4319 4433 541095837 541095951 2.350000e-44 191.0
22 TraesCS6D01G241100 chr2A 86.364 132 13 4 6248 6375 643493260 643493130 8.620000e-29 139.0
23 TraesCS6D01G241100 chr7D 93.600 125 7 1 4306 4429 21093731 21093607 1.090000e-42 185.0
24 TraesCS6D01G241100 chr5B 88.966 145 12 4 4296 4439 311600684 311600543 6.570000e-40 176.0
25 TraesCS6D01G241100 chr2B 85.315 143 14 6 6238 6375 585936581 585936441 2.400000e-29 141.0
26 TraesCS6D01G241100 chr2D 84.615 143 15 6 6238 6375 498805686 498805546 1.110000e-27 135.0


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 TraesCS6D01G241100 chr6D 343551942 343558316 6374 False 11773.00 11773 100.0000 1 6375 1 chr6D.!!$F2 6374
1 TraesCS6D01G241100 chr6A 483895395 483900956 5561 False 4178.50 5415 93.9135 748 6375 2 chr6A.!!$F1 5627
2 TraesCS6D01G241100 chr6B 518380991 518392311 11320 False 816.71 3362 91.5866 1 6375 10 chr6B.!!$F1 6374

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
479 509 0.320946 TTTAGTTTGAGGGGACGGCG 60.321 55.000 4.80 4.80 0.0 6.46 F
607 637 0.323725 GCTTGCCATCCTTCTCCCAA 60.324 55.000 0.00 0.00 0.0 4.12 F
936 5739 1.079127 CGCTCGGTCCCTCACAAAT 60.079 57.895 0.00 0.00 0.0 2.32 F
2058 6904 0.391661 CACTTGAGTATGTGGCCGCT 60.392 55.000 18.96 5.67 0.0 5.52 F
3802 8856 0.515127 ACACACACACACACAACACG 59.485 50.000 0.00 0.00 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 6241 2.266055 GACGGGGAACTGGAGCAG 59.734 66.667 0.0 0.0 42.76 4.24 R
1993 6838 3.059834 GCAAATGAACATGCAACTAAGCG 59.940 43.478 0.0 0.0 42.12 4.68 R
2196 7042 3.417069 TCTGAATTGCCGAGGAAGAAA 57.583 42.857 0.0 0.0 0.00 2.52 R
3864 8927 0.251653 TCTAGGGTCAGCGTTCTGGT 60.252 55.000 0.0 0.0 40.69 4.00 R
5555 10670 0.035056 ATTGCCCTTCTTGTCCTCCG 60.035 55.000 0.0 0.0 0.00 4.63 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 49 4.783764 TGAGCAATCTCTGTTAGTCGAA 57.216 40.909 0.00 0.00 40.03 3.71
52 53 5.724328 AGCAATCTCTGTTAGTCGAATTGA 58.276 37.500 0.00 0.00 0.00 2.57
114 137 6.672266 ATTATCATCGCCTCTTCCTTCTTA 57.328 37.500 0.00 0.00 0.00 2.10
115 138 3.802948 TCATCGCCTCTTCCTTCTTAC 57.197 47.619 0.00 0.00 0.00 2.34
138 161 7.571080 ACGAAGTAAAGTAATGGTTCCAAAA 57.429 32.000 0.00 0.00 41.94 2.44
167 190 3.329929 AAATAACCGAAGCTCTCCGTT 57.670 42.857 0.00 0.00 31.53 4.44
168 191 4.460948 AAATAACCGAAGCTCTCCGTTA 57.539 40.909 0.00 0.00 33.90 3.18
178 201 5.602628 GAAGCTCTCCGTTAAACATATCCT 58.397 41.667 0.00 0.00 0.00 3.24
188 211 6.459573 CCGTTAAACATATCCTGAAACATGGG 60.460 42.308 0.00 0.00 0.00 4.00
189 212 6.094881 CGTTAAACATATCCTGAAACATGGGT 59.905 38.462 0.00 0.00 0.00 4.51
190 213 5.920193 AAACATATCCTGAAACATGGGTG 57.080 39.130 0.00 0.00 0.00 4.61
213 236 0.974010 AGTCGCCCTTAATCGTCCCA 60.974 55.000 0.00 0.00 0.00 4.37
217 240 1.092348 GCCCTTAATCGTCCCACAAC 58.908 55.000 0.00 0.00 0.00 3.32
234 257 7.119116 GTCCCACAACATTTTGGATAAAATTCC 59.881 37.037 0.00 0.00 42.33 3.01
235 258 6.939163 CCCACAACATTTTGGATAAAATTCCA 59.061 34.615 0.00 0.00 42.33 3.53
258 281 1.700042 GGAATCGATCAGGGCCAGGT 61.700 60.000 6.18 0.00 0.00 4.00
261 284 3.790437 CGATCAGGGCCAGGTGCT 61.790 66.667 6.18 0.00 40.92 4.40
272 295 3.495983 GGGCCAGGTGCTTTATTGTTTTT 60.496 43.478 4.39 0.00 40.92 1.94
276 299 5.120674 GCCAGGTGCTTTATTGTTTTTCATC 59.879 40.000 0.00 0.00 36.87 2.92
374 397 7.874940 TCCAAAGACATGAAAATAGACAACAG 58.125 34.615 0.00 0.00 0.00 3.16
380 403 5.065218 ACATGAAAATAGACAACAGCGATCC 59.935 40.000 0.00 0.00 0.00 3.36
427 457 2.809601 CGAACGGTCGCCAGAAGG 60.810 66.667 11.19 0.00 41.08 3.46
428 458 2.654877 GAACGGTCGCCAGAAGGA 59.345 61.111 0.00 0.00 36.89 3.36
434 464 2.203788 TCGCCAGAAGGAGGTGGT 60.204 61.111 0.00 0.00 37.26 4.16
451 481 6.183360 GGAGGTGGTATTTGCGAATGATTTTA 60.183 38.462 9.60 0.00 0.00 1.52
475 505 3.576550 TGGCATTTTTAGTTTGAGGGGAC 59.423 43.478 0.00 0.00 0.00 4.46
479 509 0.320946 TTTAGTTTGAGGGGACGGCG 60.321 55.000 4.80 4.80 0.00 6.46
500 530 3.809832 CGGTTTCTTCAGAGTGACATGTT 59.190 43.478 0.00 0.00 0.00 2.71
509 539 3.123621 CAGAGTGACATGTTAGTTTCGGC 59.876 47.826 0.00 0.00 0.00 5.54
543 573 6.616260 GCAATTTTCGTTTCTAAACTGCCATG 60.616 38.462 4.24 0.00 36.77 3.66
576 606 8.251721 TCTAGTCTTAGAACTAAAACTGCCATC 58.748 37.037 9.85 0.00 33.01 3.51
601 631 1.260544 AGGTTTGCTTGCCATCCTTC 58.739 50.000 0.00 0.00 0.00 3.46
607 637 0.323725 GCTTGCCATCCTTCTCCCAA 60.324 55.000 0.00 0.00 0.00 4.12
634 3649 2.882761 GGTCGCCCAGTTAACTTTTTCT 59.117 45.455 5.07 0.00 0.00 2.52
705 3720 1.776662 ACTACGCTGCCCTCATCTTA 58.223 50.000 0.00 0.00 0.00 2.10
715 3730 3.200605 TGCCCTCATCTTATTCAAGCTGA 59.799 43.478 0.00 0.00 35.17 4.26
722 3737 7.307870 CCTCATCTTATTCAAGCTGATAAGCAC 60.308 40.741 4.45 0.00 36.57 4.40
723 3738 5.973651 TCTTATTCAAGCTGATAAGCACG 57.026 39.130 4.45 0.00 37.25 5.34
724 3739 5.419542 TCTTATTCAAGCTGATAAGCACGT 58.580 37.500 4.45 0.00 37.25 4.49
725 3740 5.874810 TCTTATTCAAGCTGATAAGCACGTT 59.125 36.000 4.45 0.00 37.25 3.99
726 3741 3.811722 TTCAAGCTGATAAGCACGTTG 57.188 42.857 4.45 0.32 37.25 4.10
727 3742 1.464608 TCAAGCTGATAAGCACGTTGC 59.535 47.619 4.45 2.28 45.46 4.17
740 3755 3.766151 GCACGTTGCATCTACTACTACA 58.234 45.455 5.30 0.00 44.26 2.74
741 3756 4.360563 GCACGTTGCATCTACTACTACAT 58.639 43.478 5.30 0.00 44.26 2.29
742 3757 4.804139 GCACGTTGCATCTACTACTACATT 59.196 41.667 5.30 0.00 44.26 2.71
743 3758 5.291128 GCACGTTGCATCTACTACTACATTT 59.709 40.000 5.30 0.00 44.26 2.32
744 3759 6.696198 CACGTTGCATCTACTACTACATTTG 58.304 40.000 0.00 0.00 0.00 2.32
745 3760 6.310467 CACGTTGCATCTACTACTACATTTGT 59.690 38.462 0.00 0.00 0.00 2.83
746 3761 7.486870 CACGTTGCATCTACTACTACATTTGTA 59.513 37.037 0.00 0.00 0.00 2.41
777 3792 2.035321 GTCTTCCTAATCTCCGAGCTGG 59.965 54.545 0.00 0.00 40.09 4.85
897 5695 2.326428 TCACTCGTTCCCCTTCTCTTT 58.674 47.619 0.00 0.00 0.00 2.52
919 5722 1.411089 CTTCGGACGCGAAGAAACG 59.589 57.895 15.93 7.81 45.73 3.60
936 5739 1.079127 CGCTCGGTCCCTCACAAAT 60.079 57.895 0.00 0.00 0.00 2.32
1425 6231 3.890674 GCTCACTACTTTGGGCGG 58.109 61.111 0.00 0.00 31.97 6.13
1519 6325 4.676196 GCTGCTTGATTCATCCGAAATTGT 60.676 41.667 0.00 0.00 34.01 2.71
1539 6345 6.642707 TTGTAGATTGGGTTTGAATTCGTT 57.357 33.333 0.04 0.00 0.00 3.85
1719 6563 3.044235 TCTGCACTATTGGACACACAG 57.956 47.619 0.00 0.00 0.00 3.66
1726 6571 5.510671 CACTATTGGACACACAGTTTGTTC 58.489 41.667 0.00 0.00 35.67 3.18
1741 6586 7.852945 CACAGTTTGTTCTCAAGTTAGACATTC 59.147 37.037 0.00 0.00 34.88 2.67
1876 6721 6.404403 CGTAGACATTGTTTGCCTCTACTCTA 60.404 42.308 8.55 0.00 34.26 2.43
1877 6722 5.725362 AGACATTGTTTGCCTCTACTCTAC 58.275 41.667 0.00 0.00 0.00 2.59
1878 6723 5.482175 AGACATTGTTTGCCTCTACTCTACT 59.518 40.000 0.00 0.00 0.00 2.57
1879 6724 6.014156 AGACATTGTTTGCCTCTACTCTACTT 60.014 38.462 0.00 0.00 0.00 2.24
1940 6785 4.216411 ACGTAGGGCAATCAGTTGTAAT 57.784 40.909 0.00 0.00 37.65 1.89
1993 6838 9.430623 GATCCCTTAATAGTCTTAGATTTGCTC 57.569 37.037 0.00 0.00 0.00 4.26
2058 6904 0.391661 CACTTGAGTATGTGGCCGCT 60.392 55.000 18.96 5.67 0.00 5.52
2196 7042 4.889409 TGCTTTCACTTGTCCTGATTCTTT 59.111 37.500 0.00 0.00 0.00 2.52
2404 7250 3.673323 CGTATGTACTCTGCAGCTTGACA 60.673 47.826 9.47 10.66 0.00 3.58
2561 7409 1.480954 AGTAATCCACGGTCGCTGATT 59.519 47.619 10.97 10.97 0.00 2.57
2857 7705 4.157840 GGTTCTTCAGTGTGTTTCCAGTTT 59.842 41.667 0.00 0.00 0.00 2.66
3124 7995 5.163622 CCGGAAGATTTTGCATGATAACTGT 60.164 40.000 0.00 0.00 0.00 3.55
3169 8040 5.869344 TGTTATGGAATATGAGTATGCGAGC 59.131 40.000 0.00 0.00 0.00 5.03
3185 8056 2.478134 GCGAGCATCCACATGTAATCTC 59.522 50.000 0.00 0.68 31.86 2.75
3188 8059 2.107204 AGCATCCACATGTAATCTCCCC 59.893 50.000 0.00 0.00 31.86 4.81
3190 8061 2.278657 TCCACATGTAATCTCCCCCA 57.721 50.000 0.00 0.00 0.00 4.96
3464 8418 4.144297 GGCATGCTTTCTGTAATATGGGA 58.856 43.478 18.92 0.00 0.00 4.37
3555 8514 1.538512 CCTGTGGTCTGTTTGATGCAG 59.461 52.381 0.00 0.00 35.43 4.41
3725 8779 3.364964 CCACCATTTTTCTTCTCGAACGG 60.365 47.826 0.00 0.00 0.00 4.44
3735 8789 4.415332 TCGAACGGCGCAGGAGAC 62.415 66.667 13.26 0.00 40.61 3.36
3796 8850 1.917782 AACGCCACACACACACACAC 61.918 55.000 0.00 0.00 0.00 3.82
3797 8851 2.394563 CGCCACACACACACACACA 61.395 57.895 0.00 0.00 0.00 3.72
3802 8856 0.515127 ACACACACACACACAACACG 59.485 50.000 0.00 0.00 0.00 4.49
3806 8860 3.199190 ACACACACAACACGCCCG 61.199 61.111 0.00 0.00 0.00 6.13
3819 8873 2.482333 CGCCCGAAACCCAAACACA 61.482 57.895 0.00 0.00 0.00 3.72
3827 8881 3.743269 CGAAACCCAAACACACTAGACCT 60.743 47.826 0.00 0.00 0.00 3.85
3864 8927 3.134574 ACAAAGGATACGACCAAAGCA 57.865 42.857 0.00 0.00 46.39 3.91
3872 8935 1.157870 ACGACCAAAGCACCAGAACG 61.158 55.000 0.00 0.00 0.00 3.95
3988 9051 2.239907 GGGCTACCTCAGATTCCACTTT 59.760 50.000 0.00 0.00 0.00 2.66
4009 9072 8.400947 CACTTTCGTATCCAATCTCATTTCATT 58.599 33.333 0.00 0.00 0.00 2.57
4010 9073 9.613428 ACTTTCGTATCCAATCTCATTTCATTA 57.387 29.630 0.00 0.00 0.00 1.90
4013 9076 9.777297 TTCGTATCCAATCTCATTTCATTATCA 57.223 29.630 0.00 0.00 0.00 2.15
4014 9077 9.777297 TCGTATCCAATCTCATTTCATTATCAA 57.223 29.630 0.00 0.00 0.00 2.57
4036 9099 4.650754 AAGATACTGCTATCGTTTCGGT 57.349 40.909 0.00 0.00 34.87 4.69
4064 9130 7.149202 TCCAAATGTCCCAAGCTACTATATT 57.851 36.000 0.00 0.00 0.00 1.28
4266 9349 6.405397 GCCAATAAGTTCGTAACCATCCAAAT 60.405 38.462 0.00 0.00 0.00 2.32
4277 9360 8.368668 TCGTAACCATCCAAATAAAAACCAAAT 58.631 29.630 0.00 0.00 0.00 2.32
4322 9420 5.681179 GCCAGAAACCAAACATACAACAACT 60.681 40.000 0.00 0.00 0.00 3.16
4323 9421 6.460399 GCCAGAAACCAAACATACAACAACTA 60.460 38.462 0.00 0.00 0.00 2.24
4324 9422 6.915843 CCAGAAACCAAACATACAACAACTAC 59.084 38.462 0.00 0.00 0.00 2.73
4325 9423 7.201785 CCAGAAACCAAACATACAACAACTACT 60.202 37.037 0.00 0.00 0.00 2.57
4326 9424 7.855904 CAGAAACCAAACATACAACAACTACTC 59.144 37.037 0.00 0.00 0.00 2.59
4327 9425 6.628919 AACCAAACATACAACAACTACTCC 57.371 37.500 0.00 0.00 0.00 3.85
4328 9426 5.067954 ACCAAACATACAACAACTACTCCC 58.932 41.667 0.00 0.00 0.00 4.30
4329 9427 5.163131 ACCAAACATACAACAACTACTCCCT 60.163 40.000 0.00 0.00 0.00 4.20
4330 9428 5.411669 CCAAACATACAACAACTACTCCCTC 59.588 44.000 0.00 0.00 0.00 4.30
4331 9429 6.231211 CAAACATACAACAACTACTCCCTCT 58.769 40.000 0.00 0.00 0.00 3.69
4332 9430 5.407407 ACATACAACAACTACTCCCTCTG 57.593 43.478 0.00 0.00 0.00 3.35
4333 9431 4.838986 ACATACAACAACTACTCCCTCTGT 59.161 41.667 0.00 0.00 0.00 3.41
4334 9432 5.307196 ACATACAACAACTACTCCCTCTGTT 59.693 40.000 0.00 0.00 0.00 3.16
4335 9433 4.338379 ACAACAACTACTCCCTCTGTTC 57.662 45.455 0.00 0.00 0.00 3.18
4336 9434 3.071167 ACAACAACTACTCCCTCTGTTCC 59.929 47.826 0.00 0.00 0.00 3.62
4337 9435 2.972348 ACAACTACTCCCTCTGTTCCA 58.028 47.619 0.00 0.00 0.00 3.53
4338 9436 3.314693 ACAACTACTCCCTCTGTTCCAA 58.685 45.455 0.00 0.00 0.00 3.53
4339 9437 3.714798 ACAACTACTCCCTCTGTTCCAAA 59.285 43.478 0.00 0.00 0.00 3.28
4340 9438 4.351111 ACAACTACTCCCTCTGTTCCAAAT 59.649 41.667 0.00 0.00 0.00 2.32
4341 9439 5.163088 ACAACTACTCCCTCTGTTCCAAATT 60.163 40.000 0.00 0.00 0.00 1.82
4342 9440 6.043938 ACAACTACTCCCTCTGTTCCAAATTA 59.956 38.462 0.00 0.00 0.00 1.40
4343 9441 6.051179 ACTACTCCCTCTGTTCCAAATTAC 57.949 41.667 0.00 0.00 0.00 1.89
4344 9442 5.785940 ACTACTCCCTCTGTTCCAAATTACT 59.214 40.000 0.00 0.00 0.00 2.24
4345 9443 5.167303 ACTCCCTCTGTTCCAAATTACTC 57.833 43.478 0.00 0.00 0.00 2.59
4346 9444 4.184629 CTCCCTCTGTTCCAAATTACTCG 58.815 47.826 0.00 0.00 0.00 4.18
4347 9445 3.581332 TCCCTCTGTTCCAAATTACTCGT 59.419 43.478 0.00 0.00 0.00 4.18
4348 9446 3.933332 CCCTCTGTTCCAAATTACTCGTC 59.067 47.826 0.00 0.00 0.00 4.20
4349 9447 3.612860 CCTCTGTTCCAAATTACTCGTCG 59.387 47.826 0.00 0.00 0.00 5.12
4350 9448 2.991190 TCTGTTCCAAATTACTCGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
4351 9449 2.734606 CTGTTCCAAATTACTCGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
4352 9450 2.734606 TGTTCCAAATTACTCGTCGCAG 59.265 45.455 0.00 0.00 0.00 5.18
4353 9451 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
4354 9452 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
4355 9453 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
4356 9454 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
4357 9455 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
4358 9456 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
4359 9457 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
4360 9458 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
4361 9459 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
4362 9460 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
4363 9461 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
4364 9462 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
4365 9463 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
4366 9464 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
4367 9465 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
4368 9466 4.982295 CGTCGCAGAAATGGATGTATCTAA 59.018 41.667 0.00 0.00 39.69 2.10
4369 9467 5.462068 CGTCGCAGAAATGGATGTATCTAAA 59.538 40.000 0.00 0.00 39.69 1.85
4370 9468 6.019075 CGTCGCAGAAATGGATGTATCTAAAA 60.019 38.462 0.00 0.00 39.69 1.52
4371 9469 7.126398 GTCGCAGAAATGGATGTATCTAAAAC 58.874 38.462 0.00 0.00 39.69 2.43
4372 9470 7.011482 GTCGCAGAAATGGATGTATCTAAAACT 59.989 37.037 0.00 0.00 39.69 2.66
4373 9471 8.201464 TCGCAGAAATGGATGTATCTAAAACTA 58.799 33.333 0.00 0.00 0.00 2.24
4374 9472 8.826710 CGCAGAAATGGATGTATCTAAAACTAA 58.173 33.333 0.00 0.00 0.00 2.24
4402 9500 6.625362 ACATCTAGATACATCCATACTTGCG 58.375 40.000 4.54 0.00 0.00 4.85
4403 9501 6.434340 ACATCTAGATACATCCATACTTGCGA 59.566 38.462 4.54 0.00 0.00 5.10
4404 9502 6.255596 TCTAGATACATCCATACTTGCGAC 57.744 41.667 0.00 0.00 0.00 5.19
4405 9503 4.937201 AGATACATCCATACTTGCGACA 57.063 40.909 0.00 0.00 0.00 4.35
4406 9504 5.276461 AGATACATCCATACTTGCGACAA 57.724 39.130 0.00 0.00 0.00 3.18
4407 9505 5.292765 AGATACATCCATACTTGCGACAAG 58.707 41.667 15.16 15.16 0.00 3.16
4408 9506 3.334583 ACATCCATACTTGCGACAAGT 57.665 42.857 22.53 22.53 0.00 3.16
4409 9507 4.465632 ACATCCATACTTGCGACAAGTA 57.534 40.909 24.52 24.52 37.18 2.24
4410 9508 4.827692 ACATCCATACTTGCGACAAGTAA 58.172 39.130 25.44 15.64 36.45 2.24
4411 9509 5.428253 ACATCCATACTTGCGACAAGTAAT 58.572 37.500 25.44 16.71 36.45 1.89
4412 9510 5.880332 ACATCCATACTTGCGACAAGTAATT 59.120 36.000 25.44 14.21 36.45 1.40
4413 9511 6.037172 ACATCCATACTTGCGACAAGTAATTC 59.963 38.462 25.44 0.00 36.45 2.17
4414 9512 4.565166 TCCATACTTGCGACAAGTAATTCG 59.435 41.667 25.44 17.44 36.45 3.34
4415 9513 4.260212 CCATACTTGCGACAAGTAATTCGG 60.260 45.833 25.44 20.47 36.45 4.30
4416 9514 3.034721 ACTTGCGACAAGTAATTCGGA 57.965 42.857 19.21 0.00 35.73 4.55
4417 9515 3.395639 ACTTGCGACAAGTAATTCGGAA 58.604 40.909 19.21 0.00 42.34 4.30
4418 9516 3.185797 ACTTGCGACAAGTAATTCGGAAC 59.814 43.478 19.21 0.00 40.13 3.62
4419 9517 6.846654 TACTTGCGACAAGTAATTCGGAACG 61.847 44.000 21.94 0.00 40.13 3.95
4537 9637 4.199310 TGATGTCCAGTTTAATAGCAGCC 58.801 43.478 0.00 0.00 0.00 4.85
4746 9849 4.938226 CCTTCAGAGTAAGGTCAATTGTCC 59.062 45.833 13.19 13.19 41.06 4.02
4805 9914 4.592778 AGGCCTGGAAATGTTTTTATGTGT 59.407 37.500 3.11 0.00 0.00 3.72
4930 10039 1.965930 GTGTGCTCGGACATTGGCA 60.966 57.895 0.00 0.00 0.00 4.92
4963 10072 0.526524 GCTCACGACAAGAGGATCGG 60.527 60.000 0.00 0.00 42.67 4.18
5032 10141 0.036952 TGCTGTCTGCTCTAGTTGCC 60.037 55.000 3.20 0.00 43.37 4.52
5047 10156 1.522258 GTTGCCGTTGAAGCATGTTTG 59.478 47.619 0.00 0.00 40.59 2.93
5100 10209 1.386533 CTGGGTCCAGCAAGCATTAG 58.613 55.000 3.86 0.00 37.24 1.73
5378 10490 3.258372 TGAATACCGAGCTGTCTGAACTT 59.742 43.478 0.00 0.00 0.00 2.66
5400 10512 4.257267 TGTGTGATGTCTCTCAAATCGT 57.743 40.909 0.00 0.00 0.00 3.73
5449 10561 6.577103 TGTCATGAACCAAAATGCTTGTTTA 58.423 32.000 0.00 0.00 0.00 2.01
5515 10630 6.919721 TCAGGAATATTTGTTTTGGCACTAC 58.080 36.000 0.00 0.00 0.00 2.73
5521 10636 1.434555 TGTTTTGGCACTACGATCCG 58.565 50.000 0.00 0.00 0.00 4.18
5555 10670 5.937975 TCATTTTCCATTCCCCATCTTTC 57.062 39.130 0.00 0.00 0.00 2.62
5572 10687 1.125093 TTCGGAGGACAAGAAGGGCA 61.125 55.000 0.00 0.00 0.00 5.36
5611 10728 6.601741 TGTGATTTTTGCAAAACAATCTCC 57.398 33.333 25.76 19.50 38.31 3.71
5691 10808 1.469940 GCATGGTACTCGAGAGGTGTG 60.470 57.143 21.68 12.71 0.00 3.82
5692 10809 1.819288 CATGGTACTCGAGAGGTGTGT 59.181 52.381 21.68 0.00 0.00 3.72
5693 10810 1.991121 TGGTACTCGAGAGGTGTGTT 58.009 50.000 21.68 0.00 0.00 3.32
5694 10811 3.144657 TGGTACTCGAGAGGTGTGTTA 57.855 47.619 21.68 0.00 0.00 2.41
5695 10812 3.079578 TGGTACTCGAGAGGTGTGTTAG 58.920 50.000 21.68 0.00 0.00 2.34
5696 10813 3.080319 GGTACTCGAGAGGTGTGTTAGT 58.920 50.000 21.68 0.00 0.00 2.24
5788 10906 6.526526 TGGTCATACTTGCACTGTAACTTAA 58.473 36.000 3.30 0.00 0.00 1.85
5799 10917 6.089820 TGCACTGTAACTTAATTACGCAGTAC 59.910 38.462 0.00 0.00 45.76 2.73
5964 11148 7.122650 TGTTTCTTAAGAATGGATCCATGGTTC 59.877 37.037 27.97 21.19 36.68 3.62
5990 11174 7.364585 CCCATTTATACTTTGGCCTTTGAATGA 60.365 37.037 3.32 0.00 0.00 2.57
6094 11360 3.118542 ACGAAGAACACGAACACCTAAC 58.881 45.455 0.00 0.00 34.70 2.34
6100 11366 1.483415 ACACGAACACCTAACAGTGGT 59.517 47.619 0.00 0.00 41.46 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.599732 ACAGAGATTGCTCATACAGTCATC 58.400 41.667 0.00 0.00 43.81 2.92
114 137 7.571080 TTTTGGAACCATTACTTTACTTCGT 57.429 32.000 0.00 0.00 0.00 3.85
115 138 9.471084 AAATTTTGGAACCATTACTTTACTTCG 57.529 29.630 0.00 0.00 0.00 3.79
138 161 5.652452 AGAGCTTCGGTTATTTAAGCCAAAT 59.348 36.000 0.00 0.17 45.32 2.32
142 165 3.560481 GGAGAGCTTCGGTTATTTAAGCC 59.440 47.826 0.00 0.00 45.32 4.35
167 190 6.726379 TCACCCATGTTTCAGGATATGTTTA 58.274 36.000 0.00 0.00 0.00 2.01
168 191 5.579047 TCACCCATGTTTCAGGATATGTTT 58.421 37.500 0.00 0.00 0.00 2.83
178 201 3.006940 GCGACTTATCACCCATGTTTCA 58.993 45.455 0.00 0.00 0.00 2.69
188 211 3.714391 ACGATTAAGGGCGACTTATCAC 58.286 45.455 0.00 0.00 41.13 3.06
189 212 3.243636 GGACGATTAAGGGCGACTTATCA 60.244 47.826 0.00 0.00 41.13 2.15
190 213 3.315418 GGACGATTAAGGGCGACTTATC 58.685 50.000 0.00 0.00 41.13 1.75
234 257 1.069765 CCCTGATCGATTCCCGGTG 59.930 63.158 0.00 0.00 39.14 4.94
235 258 2.808206 GCCCTGATCGATTCCCGGT 61.808 63.158 0.00 0.00 39.14 5.28
258 281 7.966246 ATTGCAGATGAAAAACAATAAAGCA 57.034 28.000 0.00 0.00 0.00 3.91
285 308 0.618458 AGAAGGAGGTTAATGCGGCA 59.382 50.000 4.58 4.58 0.00 5.69
288 311 6.202954 CCTTTACATAGAAGGAGGTTAATGCG 59.797 42.308 0.00 0.00 45.25 4.73
299 322 4.898861 AGCTCTCTCCCTTTACATAGAAGG 59.101 45.833 0.00 0.00 42.68 3.46
374 397 5.652744 TTATAAGAAGCTTTTCGGATCGC 57.347 39.130 0.00 0.00 0.00 4.58
380 403 8.290325 GGGTCCATTATTATAAGAAGCTTTTCG 58.710 37.037 0.00 0.00 0.00 3.46
421 451 2.009774 CGCAAATACCACCTCCTTCTG 58.990 52.381 0.00 0.00 0.00 3.02
422 452 1.906574 TCGCAAATACCACCTCCTTCT 59.093 47.619 0.00 0.00 0.00 2.85
424 454 2.871096 TTCGCAAATACCACCTCCTT 57.129 45.000 0.00 0.00 0.00 3.36
425 455 2.238646 TCATTCGCAAATACCACCTCCT 59.761 45.455 0.00 0.00 0.00 3.69
426 456 2.639065 TCATTCGCAAATACCACCTCC 58.361 47.619 0.00 0.00 0.00 4.30
427 457 4.900635 AATCATTCGCAAATACCACCTC 57.099 40.909 0.00 0.00 0.00 3.85
428 458 5.659440 AAAATCATTCGCAAATACCACCT 57.341 34.783 0.00 0.00 0.00 4.00
434 464 6.201226 TGCCACTAAAATCATTCGCAAATA 57.799 33.333 0.00 0.00 0.00 1.40
451 481 3.578282 CCCCTCAAACTAAAAATGCCACT 59.422 43.478 0.00 0.00 0.00 4.00
475 505 0.319555 TCACTCTGAAGAAACCGCCG 60.320 55.000 0.00 0.00 0.00 6.46
479 509 5.992217 ACTAACATGTCACTCTGAAGAAACC 59.008 40.000 0.00 0.00 0.00 3.27
500 530 0.249398 GCCTTCTCTGGCCGAAACTA 59.751 55.000 0.00 0.00 46.82 2.24
509 539 3.923017 AACGAAAATTGCCTTCTCTGG 57.077 42.857 0.00 0.00 0.00 3.86
526 556 3.915437 AACCATGGCAGTTTAGAAACG 57.085 42.857 13.04 0.00 43.51 3.60
582 612 1.203100 AGAAGGATGGCAAGCAAACCT 60.203 47.619 0.00 0.00 0.00 3.50
583 613 1.203287 GAGAAGGATGGCAAGCAAACC 59.797 52.381 0.00 0.00 0.00 3.27
584 614 1.203287 GGAGAAGGATGGCAAGCAAAC 59.797 52.381 0.00 0.00 0.00 2.93
651 3666 9.513906 AGGACCTGATCTCATATATCATATACG 57.486 37.037 0.00 0.00 33.08 3.06
655 3670 9.418839 CAAGAGGACCTGATCTCATATATCATA 57.581 37.037 0.00 0.00 33.08 2.15
656 3671 8.121185 TCAAGAGGACCTGATCTCATATATCAT 58.879 37.037 0.00 0.00 33.08 2.45
657 3672 7.395772 GTCAAGAGGACCTGATCTCATATATCA 59.604 40.741 0.00 0.00 40.83 2.15
658 3673 7.771183 GTCAAGAGGACCTGATCTCATATATC 58.229 42.308 0.00 0.00 40.83 1.63
659 3674 7.716799 GTCAAGAGGACCTGATCTCATATAT 57.283 40.000 0.00 0.00 40.83 0.86
715 3730 5.263968 AGTAGTAGATGCAACGTGCTTAT 57.736 39.130 10.54 5.30 45.31 1.73
722 3737 6.887376 ACAAATGTAGTAGTAGATGCAACG 57.113 37.500 0.00 0.00 0.00 4.10
727 3742 9.587772 GGGCATATACAAATGTAGTAGTAGATG 57.412 37.037 0.00 0.00 38.51 2.90
728 3743 8.467598 CGGGCATATACAAATGTAGTAGTAGAT 58.532 37.037 0.00 0.00 33.52 1.98
729 3744 7.449395 ACGGGCATATACAAATGTAGTAGTAGA 59.551 37.037 0.00 0.00 33.52 2.59
730 3745 7.541091 CACGGGCATATACAAATGTAGTAGTAG 59.459 40.741 0.00 0.00 33.52 2.57
731 3746 7.014518 ACACGGGCATATACAAATGTAGTAGTA 59.985 37.037 0.00 0.00 33.52 1.82
732 3747 6.183360 ACACGGGCATATACAAATGTAGTAGT 60.183 38.462 0.00 0.00 33.52 2.73
733 3748 6.220930 ACACGGGCATATACAAATGTAGTAG 58.779 40.000 0.00 0.00 33.52 2.57
734 3749 6.041182 AGACACGGGCATATACAAATGTAGTA 59.959 38.462 0.00 0.00 33.52 1.82
735 3750 5.031066 ACACGGGCATATACAAATGTAGT 57.969 39.130 0.00 0.00 33.52 2.73
736 3751 5.297547 AGACACGGGCATATACAAATGTAG 58.702 41.667 0.00 0.00 33.52 2.74
737 3752 5.284861 AGACACGGGCATATACAAATGTA 57.715 39.130 0.00 0.00 34.67 2.29
738 3753 4.150897 AGACACGGGCATATACAAATGT 57.849 40.909 0.00 0.00 0.00 2.71
739 3754 4.024048 GGAAGACACGGGCATATACAAATG 60.024 45.833 0.00 0.00 0.00 2.32
740 3755 4.134563 GGAAGACACGGGCATATACAAAT 58.865 43.478 0.00 0.00 0.00 2.32
741 3756 3.199071 AGGAAGACACGGGCATATACAAA 59.801 43.478 0.00 0.00 0.00 2.83
742 3757 2.769663 AGGAAGACACGGGCATATACAA 59.230 45.455 0.00 0.00 0.00 2.41
743 3758 2.394632 AGGAAGACACGGGCATATACA 58.605 47.619 0.00 0.00 0.00 2.29
744 3759 4.595762 TTAGGAAGACACGGGCATATAC 57.404 45.455 0.00 0.00 0.00 1.47
745 3760 5.084519 AGATTAGGAAGACACGGGCATATA 58.915 41.667 0.00 0.00 0.00 0.86
746 3761 3.904339 AGATTAGGAAGACACGGGCATAT 59.096 43.478 0.00 0.00 0.00 1.78
804 5596 0.739813 GACACCTTTCATCGGGTCCG 60.740 60.000 2.52 2.52 41.35 4.79
805 5599 0.739813 CGACACCTTTCATCGGGTCC 60.740 60.000 0.00 0.00 32.95 4.46
919 5722 1.480954 TCTATTTGTGAGGGACCGAGC 59.519 52.381 0.00 0.00 0.00 5.03
1435 6241 2.266055 GACGGGGAACTGGAGCAG 59.734 66.667 0.00 0.00 42.76 4.24
1519 6325 6.001460 AGACAACGAATTCAAACCCAATCTA 58.999 36.000 6.22 0.00 0.00 1.98
1539 6345 7.338703 AGTCGTGGTAATATGAACTCTAAGACA 59.661 37.037 0.00 0.00 0.00 3.41
1719 6563 7.173863 TCGAATGTCTAACTTGAGAACAAAC 57.826 36.000 0.00 0.00 35.49 2.93
1726 6571 9.521503 TTATCTGATTCGAATGTCTAACTTGAG 57.478 33.333 16.96 0.00 0.00 3.02
1993 6838 3.059834 GCAAATGAACATGCAACTAAGCG 59.940 43.478 0.00 0.00 42.12 4.68
2196 7042 3.417069 TCTGAATTGCCGAGGAAGAAA 57.583 42.857 0.00 0.00 0.00 2.52
2404 7250 8.706322 AACAGTTGTATTAAAGTTCCAGGAAT 57.294 30.769 4.80 0.00 0.00 3.01
2440 7288 3.876914 TCTTCTTGTGTGCACAACCTAAG 59.123 43.478 23.59 20.96 45.42 2.18
2442 7290 3.552132 TCTTCTTGTGTGCACAACCTA 57.448 42.857 23.59 6.26 45.42 3.08
2561 7409 7.977293 CACAAATCTTGGAATGCAAGATATTGA 59.023 33.333 31.81 13.44 45.48 2.57
2626 7474 4.337555 CACCAGATTCCTCAAATAAGGCAG 59.662 45.833 0.00 0.00 36.29 4.85
2633 7481 7.004086 TGTAAGTTTCACCAGATTCCTCAAAT 58.996 34.615 0.00 0.00 0.00 2.32
2857 7705 9.396022 ACAAAAGAAGAGACAGACAAGATTAAA 57.604 29.630 0.00 0.00 0.00 1.52
2880 7728 6.093495 CGGGAAGCAGATTTCATTAGTTACAA 59.907 38.462 0.00 0.00 0.00 2.41
3169 8040 2.442878 TGGGGGAGATTACATGTGGATG 59.557 50.000 9.11 0.00 35.49 3.51
3185 8056 2.514160 AGCTATTAAACCTTCCTGGGGG 59.486 50.000 0.00 0.00 41.11 5.40
3188 8059 7.610305 TCAACTTAAGCTATTAAACCTTCCTGG 59.390 37.037 1.29 0.00 42.93 4.45
3190 8061 9.011095 GTTCAACTTAAGCTATTAAACCTTCCT 57.989 33.333 1.29 0.00 30.59 3.36
3412 8366 7.605449 AGCTAATATTCAAAACTGTTGCATGT 58.395 30.769 0.00 0.00 0.00 3.21
3464 8418 7.986889 GCCATATTCCATAATCAAACCAACTTT 59.013 33.333 0.00 0.00 0.00 2.66
3555 8514 8.636213 TGGTGAGCTACTATTTACTATAACACC 58.364 37.037 0.00 0.00 40.90 4.16
3735 8789 7.015226 TCTTATTAATGAAATGACACGCAGG 57.985 36.000 0.00 0.00 0.00 4.85
3796 8850 2.005960 TTTGGGTTTCGGGCGTGTTG 62.006 55.000 0.00 0.00 0.00 3.33
3797 8851 1.753463 TTTGGGTTTCGGGCGTGTT 60.753 52.632 0.00 0.00 0.00 3.32
3802 8856 1.066752 GTGTGTTTGGGTTTCGGGC 59.933 57.895 0.00 0.00 0.00 6.13
3806 8860 3.816994 AGGTCTAGTGTGTTTGGGTTTC 58.183 45.455 0.00 0.00 0.00 2.78
3819 8873 3.312890 AGCATGGCTCATAAGGTCTAGT 58.687 45.455 0.00 0.00 30.62 2.57
3827 8881 4.082081 CCTTTGTTCAAGCATGGCTCATAA 60.082 41.667 0.00 0.00 38.25 1.90
3864 8927 0.251653 TCTAGGGTCAGCGTTCTGGT 60.252 55.000 0.00 0.00 40.69 4.00
3927 8990 1.591280 GGGTGGTAGAGGAGGAGGGA 61.591 65.000 0.00 0.00 0.00 4.20
3988 9051 9.777297 TTGATAATGAAATGAGATTGGATACGA 57.223 29.630 0.00 0.00 42.51 3.43
4009 9072 7.381408 CCGAAACGATAGCAGTATCTTTTGATA 59.619 37.037 0.00 0.00 37.29 2.15
4010 9073 6.201044 CCGAAACGATAGCAGTATCTTTTGAT 59.799 38.462 0.00 0.00 37.29 2.57
4011 9074 5.518847 CCGAAACGATAGCAGTATCTTTTGA 59.481 40.000 0.00 0.00 37.29 2.69
4012 9075 5.291128 ACCGAAACGATAGCAGTATCTTTTG 59.709 40.000 0.00 2.46 37.29 2.44
4013 9076 5.291128 CACCGAAACGATAGCAGTATCTTTT 59.709 40.000 0.00 0.00 38.93 2.27
4014 9077 4.804139 CACCGAAACGATAGCAGTATCTTT 59.196 41.667 0.00 0.00 42.67 2.52
4015 9078 4.142227 ACACCGAAACGATAGCAGTATCTT 60.142 41.667 0.00 0.00 42.67 2.40
4016 9079 3.380637 ACACCGAAACGATAGCAGTATCT 59.619 43.478 0.00 0.00 42.67 1.98
4017 9080 3.703420 ACACCGAAACGATAGCAGTATC 58.297 45.455 0.00 0.00 42.67 2.24
4018 9081 3.795623 ACACCGAAACGATAGCAGTAT 57.204 42.857 0.00 0.00 42.67 2.12
4019 9082 3.581024 AACACCGAAACGATAGCAGTA 57.419 42.857 0.00 0.00 42.67 2.74
4020 9083 2.450609 AACACCGAAACGATAGCAGT 57.549 45.000 0.00 0.00 42.67 4.40
4021 9084 2.093783 GGAAACACCGAAACGATAGCAG 59.906 50.000 0.00 0.00 42.67 4.24
4022 9085 2.070783 GGAAACACCGAAACGATAGCA 58.929 47.619 0.00 0.00 42.67 3.49
4023 9086 2.070783 TGGAAACACCGAAACGATAGC 58.929 47.619 0.00 0.00 42.61 2.97
4024 9087 4.735662 TTTGGAAACACCGAAACGATAG 57.264 40.909 0.00 0.00 42.67 2.08
4036 9099 2.676748 AGCTTGGGACATTTGGAAACA 58.323 42.857 0.00 0.00 39.30 2.83
4064 9130 5.123227 CGAAAAGGCCTCAATACCTTGATA 58.877 41.667 5.23 0.00 45.62 2.15
4277 9360 5.130477 TGGCCAAAATGTACCTTACCAAAAA 59.870 36.000 0.61 0.00 0.00 1.94
4322 9420 5.105473 CGAGTAATTTGGAACAGAGGGAGTA 60.105 44.000 0.00 0.00 42.39 2.59
4323 9421 4.322801 CGAGTAATTTGGAACAGAGGGAGT 60.323 45.833 0.00 0.00 42.39 3.85
4324 9422 4.184629 CGAGTAATTTGGAACAGAGGGAG 58.815 47.826 0.00 0.00 42.39 4.30
4325 9423 3.581332 ACGAGTAATTTGGAACAGAGGGA 59.419 43.478 0.00 0.00 42.39 4.20
4326 9424 3.933332 GACGAGTAATTTGGAACAGAGGG 59.067 47.826 0.00 0.00 42.39 4.30
4327 9425 3.612860 CGACGAGTAATTTGGAACAGAGG 59.387 47.826 0.00 0.00 42.39 3.69
4328 9426 3.060895 GCGACGAGTAATTTGGAACAGAG 59.939 47.826 0.00 0.00 42.39 3.35
4329 9427 2.991190 GCGACGAGTAATTTGGAACAGA 59.009 45.455 0.00 0.00 42.39 3.41
4330 9428 2.734606 TGCGACGAGTAATTTGGAACAG 59.265 45.455 0.00 0.00 42.39 3.16
4331 9429 2.734606 CTGCGACGAGTAATTTGGAACA 59.265 45.455 0.00 0.00 0.00 3.18
4332 9430 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
4333 9431 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
4334 9432 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
4335 9433 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
4336 9434 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
4337 9435 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
4338 9436 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
4339 9437 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
4340 9438 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
4341 9439 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
4342 9440 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
4343 9441 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
4344 9442 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
4345 9443 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
4346 9444 6.844696 TTTAGATACATCCATTTCTGCGAC 57.155 37.500 0.00 0.00 0.00 5.19
4347 9445 7.047891 AGTTTTAGATACATCCATTTCTGCGA 58.952 34.615 0.00 0.00 0.00 5.10
4348 9446 7.251704 AGTTTTAGATACATCCATTTCTGCG 57.748 36.000 0.00 0.00 0.00 5.18
4376 9474 8.409371 CGCAAGTATGGATGTATCTAGATGTAT 58.591 37.037 15.79 9.11 0.00 2.29
4377 9475 7.610305 TCGCAAGTATGGATGTATCTAGATGTA 59.390 37.037 15.79 4.44 39.48 2.29
4378 9476 6.434340 TCGCAAGTATGGATGTATCTAGATGT 59.566 38.462 15.79 1.25 39.48 3.06
4379 9477 6.749578 GTCGCAAGTATGGATGTATCTAGATG 59.250 42.308 15.79 0.00 39.48 2.90
4380 9478 6.434340 TGTCGCAAGTATGGATGTATCTAGAT 59.566 38.462 10.73 10.73 39.48 1.98
4381 9479 5.768164 TGTCGCAAGTATGGATGTATCTAGA 59.232 40.000 0.00 0.00 39.48 2.43
4382 9480 6.013842 TGTCGCAAGTATGGATGTATCTAG 57.986 41.667 0.00 0.00 39.48 2.43
4383 9481 6.040504 ACTTGTCGCAAGTATGGATGTATCTA 59.959 38.462 19.21 0.00 39.48 1.98
4384 9482 4.937201 TGTCGCAAGTATGGATGTATCT 57.063 40.909 0.00 0.00 39.48 1.98
4385 9483 5.050490 ACTTGTCGCAAGTATGGATGTATC 58.950 41.667 19.21 0.00 39.48 2.24
4386 9484 5.023533 ACTTGTCGCAAGTATGGATGTAT 57.976 39.130 19.21 0.00 39.48 2.29
4387 9485 4.465632 ACTTGTCGCAAGTATGGATGTA 57.534 40.909 19.21 0.00 39.48 2.29
4388 9486 3.334583 ACTTGTCGCAAGTATGGATGT 57.665 42.857 19.21 0.00 39.48 3.06
4389 9487 5.991328 ATTACTTGTCGCAAGTATGGATG 57.009 39.130 23.59 2.90 33.27 3.51
4390 9488 5.234329 CGAATTACTTGTCGCAAGTATGGAT 59.766 40.000 23.59 15.77 33.27 3.41
4391 9489 4.565166 CGAATTACTTGTCGCAAGTATGGA 59.435 41.667 23.59 14.66 33.27 3.41
4392 9490 4.260212 CCGAATTACTTGTCGCAAGTATGG 60.260 45.833 23.59 19.57 35.93 2.74
4393 9491 4.565166 TCCGAATTACTTGTCGCAAGTATG 59.435 41.667 23.59 16.51 35.93 2.39
4394 9492 4.751060 TCCGAATTACTTGTCGCAAGTAT 58.249 39.130 23.59 14.96 35.93 2.12
4395 9493 4.177165 TCCGAATTACTTGTCGCAAGTA 57.823 40.909 20.95 20.95 35.93 2.24
4396 9494 3.034721 TCCGAATTACTTGTCGCAAGT 57.965 42.857 22.53 22.53 35.93 3.16
4397 9495 3.720920 CGTTCCGAATTACTTGTCGCAAG 60.721 47.826 15.16 15.16 35.93 4.01
4398 9496 2.156117 CGTTCCGAATTACTTGTCGCAA 59.844 45.455 0.00 0.00 35.93 4.85
4399 9497 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
4400 9498 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
4401 9499 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
4402 9500 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4403 9501 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4404 9502 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4405 9503 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4406 9504 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4407 9505 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4408 9506 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4409 9507 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
4410 9508 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
4411 9509 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
4412 9510 0.251297 TTGTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
4413 9511 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
4414 9512 0.535797 CCTTGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
4415 9513 0.108281 GCCTTGTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
4416 9514 0.544595 AGCCTTGTACTCCCTCCGTT 60.545 55.000 0.00 0.00 0.00 4.44
4417 9515 0.333993 TAGCCTTGTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
4418 9516 1.033574 CTAGCCTTGTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
4419 9517 2.456073 TCTAGCCTTGTACTCCCTCC 57.544 55.000 0.00 0.00 0.00 4.30
4420 9518 3.367321 ACTTCTAGCCTTGTACTCCCTC 58.633 50.000 0.00 0.00 0.00 4.30
4421 9519 3.476485 ACTTCTAGCCTTGTACTCCCT 57.524 47.619 0.00 0.00 0.00 4.20
4422 9520 5.672421 TTTACTTCTAGCCTTGTACTCCC 57.328 43.478 0.00 0.00 0.00 4.30
4690 9793 7.174946 ACGGACATTAATGAAGTTTCTGAATGT 59.825 33.333 22.16 14.00 37.26 2.71
4805 9914 3.929955 TGGCAATGATACACCATCTGA 57.070 42.857 0.00 0.00 34.46 3.27
4930 10039 1.194547 CGTGAGCGTGCAGTTAATGTT 59.805 47.619 0.00 0.00 0.00 2.71
5032 10141 0.958091 TCCCCAAACATGCTTCAACG 59.042 50.000 0.00 0.00 0.00 4.10
5047 10156 3.232720 TGTGGGTTAGTTTTCTTCCCC 57.767 47.619 0.00 0.00 39.95 4.81
5100 10209 3.950869 GTGGAGAAGTTACCCCACC 57.049 57.895 0.00 0.00 42.30 4.61
5176 10288 3.861276 TCAGCCATTGAATGAGCTTTG 57.139 42.857 15.35 8.94 35.54 2.77
5378 10490 4.631131 ACGATTTGAGAGACATCACACAA 58.369 39.130 0.00 0.00 0.00 3.33
5400 10512 0.764890 CCTTCACCCCAACAGACTGA 59.235 55.000 10.08 0.00 0.00 3.41
5449 10561 1.322442 GGCAGCTCCAAACTTCACTT 58.678 50.000 0.00 0.00 34.01 3.16
5515 10630 1.552348 GATTTCTCGCCAGCGGATCG 61.552 60.000 12.71 0.00 40.25 3.69
5521 10636 2.164219 TGGAAAATGATTTCTCGCCAGC 59.836 45.455 0.00 0.00 43.65 4.85
5555 10670 0.035056 ATTGCCCTTCTTGTCCTCCG 60.035 55.000 0.00 0.00 0.00 4.63
5596 10711 7.504403 TGAAAAATAGGGAGATTGTTTTGCAA 58.496 30.769 0.00 0.00 41.89 4.08
5598 10713 7.961325 TTGAAAAATAGGGAGATTGTTTTGC 57.039 32.000 0.00 0.00 0.00 3.68
5611 10728 7.603404 TGATGCTTCCAACAATTGAAAAATAGG 59.397 33.333 13.59 3.20 0.00 2.57
5642 10759 4.105486 GAGCGCTTAATTTTCCATTCACC 58.895 43.478 13.26 0.00 0.00 4.02
5691 10808 4.251268 CCCCTACTACAGCAACAACTAAC 58.749 47.826 0.00 0.00 0.00 2.34
5692 10809 3.262405 CCCCCTACTACAGCAACAACTAA 59.738 47.826 0.00 0.00 0.00 2.24
5693 10810 2.835764 CCCCCTACTACAGCAACAACTA 59.164 50.000 0.00 0.00 0.00 2.24
5694 10811 1.628846 CCCCCTACTACAGCAACAACT 59.371 52.381 0.00 0.00 0.00 3.16
5695 10812 1.626825 TCCCCCTACTACAGCAACAAC 59.373 52.381 0.00 0.00 0.00 3.32
5696 10813 2.032965 TCCCCCTACTACAGCAACAA 57.967 50.000 0.00 0.00 0.00 2.83
5799 10917 6.841443 AAATCATTCGATCTTGACTAGCAG 57.159 37.500 0.00 0.00 0.00 4.24
5857 10988 0.934436 CGGCAACAAGTGAAAAGGCG 60.934 55.000 0.00 0.00 38.61 5.52
5917 11048 3.828451 CAGTCAAACAGGGATGGAAATGT 59.172 43.478 0.00 0.00 0.00 2.71
5964 11148 5.930837 TCAAAGGCCAAAGTATAAATGGG 57.069 39.130 5.01 0.00 34.71 4.00
5990 11174 5.200483 TCTGAGAAGTTGGGTTTTCAACAT 58.800 37.500 9.85 0.00 46.74 2.71
6000 11184 5.706916 CACATTTGAATCTGAGAAGTTGGG 58.293 41.667 0.00 0.00 0.00 4.12
6053 11317 6.390048 TCGTAGAGGGAGATGTATTAGGAT 57.610 41.667 0.00 0.00 0.00 3.24
6100 11366 5.128827 CCCTCATGTTTAGCTAGGTTCTGTA 59.871 44.000 0.00 0.00 0.00 2.74
6117 11407 2.825836 GCCGCCAACTCCCTCATG 60.826 66.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.