Multiple sequence alignment - TraesCS5D01G271600

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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 TraesCS5D01G271600 chr5D 100.000 5120 0 0 1 5120 375195750 375190631 0.000000e+00 9455.0
1 TraesCS5D01G271600 chr5D 83.491 212 35 0 1424 1635 375194297 375194086 1.120000e-46 198.0
2 TraesCS5D01G271600 chr5D 83.491 212 35 0 1454 1665 375194327 375194116 1.120000e-46 198.0
3 TraesCS5D01G271600 chr5D 97.143 35 1 0 4969 5003 351335589 351335623 5.540000e-05 60.2
4 TraesCS5D01G271600 chr5D 96.970 33 1 0 4970 5002 469062744 469062776 7.160000e-04 56.5
5 TraesCS5D01G271600 chr5A 93.151 3037 133 21 1424 4445 476605062 476602086 0.000000e+00 4386.0
6 TraesCS5D01G271600 chr5A 90.773 1539 95 27 154 1665 476606369 476604851 0.000000e+00 2012.0
7 TraesCS5D01G271600 chr5A 90.657 289 15 6 4712 4991 476599989 476599704 1.740000e-99 374.0
8 TraesCS5D01G271600 chr5A 89.370 254 13 3 4465 4708 476600295 476600046 1.790000e-79 307.0
9 TraesCS5D01G271600 chr5A 83.568 213 33 2 1454 1665 476605092 476604881 1.120000e-46 198.0
10 TraesCS5D01G271600 chr5B 95.040 2016 84 8 1424 3430 447843017 447841009 0.000000e+00 3155.0
11 TraesCS5D01G271600 chr5B 90.263 1674 101 34 1 1647 447844462 447842824 0.000000e+00 2132.0
12 TraesCS5D01G271600 chr5B 90.426 1525 93 25 3461 4971 447841011 447839526 0.000000e+00 1958.0
13 TraesCS5D01G271600 chr5B 78.505 214 42 2 1424 1635 447842987 447842776 2.490000e-28 137.0
14 TraesCS5D01G271600 chr5B 100.000 29 0 0 4974 5002 405764852 405764824 3.000000e-03 54.7
15 TraesCS5D01G271600 chr7B 75.354 495 105 15 2584 3070 191777119 191776634 6.670000e-54 222.0
16 TraesCS5D01G271600 chr7B 75.942 345 70 12 3773 4109 191775875 191775536 1.140000e-36 165.0
17 TraesCS5D01G271600 chr7A 75.152 495 108 12 2586 3070 222499210 222499699 8.630000e-53 219.0
18 TraesCS5D01G271600 chr7A 75.073 341 80 5 3773 4109 222500382 222500721 2.470000e-33 154.0
19 TraesCS5D01G271600 chr7D 76.984 252 50 7 3773 4020 209793612 209793859 2.490000e-28 137.0
20 TraesCS5D01G271600 chr1A 96.970 33 1 0 4970 5002 373311984 373311952 7.160000e-04 56.5
21 TraesCS5D01G271600 chr4B 100.000 29 0 0 4974 5002 613320182 613320154 3.000000e-03 54.7
22 TraesCS5D01G271600 chr1D 100.000 29 0 0 4974 5002 87661037 87661065 3.000000e-03 54.7
23 TraesCS5D01G271600 chr1D 100.000 29 0 0 4974 5002 329311597 329311569 3.000000e-03 54.7
24 TraesCS5D01G271600 chr1D 100.000 29 0 0 4974 5002 431708817 431708789 3.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G271600 chr5D 375190631 375195750 5119 True 3283.666667 9455 88.9940 1 5120 3 chr5D.!!$R1 5119
1 TraesCS5D01G271600 chr5A 476599704 476606369 6665 True 1455.400000 4386 89.5038 154 4991 5 chr5A.!!$R1 4837
2 TraesCS5D01G271600 chr5B 447839526 447844462 4936 True 1845.500000 3155 88.5585 1 4971 4 chr5B.!!$R2 4970

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
369 379 0.250727 TACAGCTTTGTGTCCCTGGC 60.251 55.0 0.00 0.0 31.46 4.85 F
646 657 0.743345 AGCTGTTTTATCCGGCGTCC 60.743 55.0 6.01 0.0 39.23 4.79 F
655 666 0.962489 ATCCGGCGTCCTATCTCTTG 59.038 55.0 6.01 0.0 0.00 3.02 F
2341 2403 0.611618 TGAATTCCGGTGGCAAGCAT 60.612 50.0 0.00 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1549 2.915349 CCTTATCATCAGCAGCTGTGT 58.085 47.619 22.10 9.59 32.61 3.72 R
2093 2155 3.363627 TCATGGCCATGTGCAGAATAAA 58.636 40.909 38.18 17.48 43.89 1.40 R
2648 2711 3.732048 ATGTCCTAACGGTTTCCCAAT 57.268 42.857 0.00 0.00 0.00 3.16 R
4248 4322 0.833949 GGGGGCAAAGGAAACAACAA 59.166 50.000 0.00 0.00 0.00 2.83 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
103 104 6.706055 TCGTAAAATTCAGTTAGTCAGCTG 57.294 37.500 7.63 7.63 34.50 4.24
107 108 6.551385 AAAATTCAGTTAGTCAGCTGTCTG 57.449 37.500 21.65 17.27 41.67 3.51
175 181 1.559149 GCCGTTTGCTTGCAACCATG 61.559 55.000 7.60 0.39 36.87 3.66
187 193 1.372582 CAACCATGTGGATCGGAGTG 58.627 55.000 5.96 0.00 38.94 3.51
188 194 1.066215 CAACCATGTGGATCGGAGTGA 60.066 52.381 5.96 0.00 38.94 3.41
189 195 0.826715 ACCATGTGGATCGGAGTGAG 59.173 55.000 5.96 0.00 38.94 3.51
190 196 0.826715 CCATGTGGATCGGAGTGAGT 59.173 55.000 0.00 0.00 37.39 3.41
199 205 0.881796 TCGGAGTGAGTACTGCACTG 59.118 55.000 23.83 14.81 45.94 3.66
293 303 6.308282 GTCCATTGTTCTTAGAGTCAAGTACG 59.692 42.308 0.00 0.00 30.76 3.67
298 308 3.332919 TCTTAGAGTCAAGTACGTCGCT 58.667 45.455 0.00 0.00 0.00 4.93
301 311 1.071567 GAGTCAAGTACGTCGCTGGC 61.072 60.000 0.00 0.00 0.00 4.85
337 347 3.165071 TGGTACAGCTTGTCAGATCTCA 58.835 45.455 0.00 0.00 0.00 3.27
339 349 3.056536 GGTACAGCTTGTCAGATCTCACA 60.057 47.826 0.00 0.00 0.00 3.58
341 351 2.632028 ACAGCTTGTCAGATCTCACAGT 59.368 45.455 0.00 0.00 0.00 3.55
343 353 4.063689 CAGCTTGTCAGATCTCACAGTTT 58.936 43.478 0.00 0.00 0.00 2.66
344 354 4.152045 CAGCTTGTCAGATCTCACAGTTTC 59.848 45.833 0.00 0.00 0.00 2.78
345 355 4.060900 GCTTGTCAGATCTCACAGTTTCA 58.939 43.478 0.00 0.00 0.00 2.69
346 356 4.152045 GCTTGTCAGATCTCACAGTTTCAG 59.848 45.833 0.00 0.00 0.00 3.02
351 361 4.524328 TCAGATCTCACAGTTTCAGCAGTA 59.476 41.667 0.00 0.00 0.00 2.74
352 362 4.624882 CAGATCTCACAGTTTCAGCAGTAC 59.375 45.833 0.00 0.00 0.00 2.73
353 363 4.281941 AGATCTCACAGTTTCAGCAGTACA 59.718 41.667 0.00 0.00 0.00 2.90
355 365 2.478134 CTCACAGTTTCAGCAGTACAGC 59.522 50.000 1.29 1.29 0.00 4.40
357 367 2.874701 CACAGTTTCAGCAGTACAGCTT 59.125 45.455 10.45 0.00 43.70 3.74
358 368 3.313526 CACAGTTTCAGCAGTACAGCTTT 59.686 43.478 10.45 0.00 43.70 3.51
359 369 3.313526 ACAGTTTCAGCAGTACAGCTTTG 59.686 43.478 10.45 1.50 43.70 2.77
360 370 3.313526 CAGTTTCAGCAGTACAGCTTTGT 59.686 43.478 10.45 0.00 43.70 2.83
361 371 3.313526 AGTTTCAGCAGTACAGCTTTGTG 59.686 43.478 10.45 0.36 43.70 3.33
363 373 2.483876 TCAGCAGTACAGCTTTGTGTC 58.516 47.619 10.45 0.00 43.70 3.67
364 374 1.532868 CAGCAGTACAGCTTTGTGTCC 59.467 52.381 10.45 0.00 43.70 4.02
365 375 0.875059 GCAGTACAGCTTTGTGTCCC 59.125 55.000 2.52 0.00 31.46 4.46
366 376 1.543429 GCAGTACAGCTTTGTGTCCCT 60.543 52.381 2.52 0.00 31.46 4.20
367 377 2.146342 CAGTACAGCTTTGTGTCCCTG 58.854 52.381 0.00 0.00 31.46 4.45
368 378 1.072331 AGTACAGCTTTGTGTCCCTGG 59.928 52.381 0.00 0.00 31.46 4.45
369 379 0.250727 TACAGCTTTGTGTCCCTGGC 60.251 55.000 0.00 0.00 31.46 4.85
370 380 2.281761 AGCTTTGTGTCCCTGGCG 60.282 61.111 0.00 0.00 0.00 5.69
371 381 4.043200 GCTTTGTGTCCCTGGCGC 62.043 66.667 0.00 0.00 0.00 6.53
375 385 4.641645 TGTGTCCCTGGCGCTTGG 62.642 66.667 7.64 9.93 0.00 3.61
442 452 1.443194 CAACGGTCGTACACCCTCG 60.443 63.158 8.36 0.00 43.31 4.63
479 489 3.256960 GCCTCCCAACCACCTCCA 61.257 66.667 0.00 0.00 0.00 3.86
515 526 4.882842 TTGCACTAGGAGACACATTACA 57.117 40.909 0.00 0.00 0.00 2.41
589 600 3.243873 TGTCTTTTGGTGTGTGTTTTGCA 60.244 39.130 0.00 0.00 0.00 4.08
625 636 4.042311 TCTCGAGGCTTGATAGAGGAGTAT 59.958 45.833 13.56 0.00 0.00 2.12
635 646 7.713073 GCTTGATAGAGGAGTATTAGCTGTTTT 59.287 37.037 0.00 0.00 0.00 2.43
643 654 4.056050 AGTATTAGCTGTTTTATCCGGCG 58.944 43.478 0.00 0.00 39.23 6.46
646 657 0.743345 AGCTGTTTTATCCGGCGTCC 60.743 55.000 6.01 0.00 39.23 4.79
648 659 1.472026 GCTGTTTTATCCGGCGTCCTA 60.472 52.381 6.01 0.00 0.00 2.94
650 661 3.057734 CTGTTTTATCCGGCGTCCTATC 58.942 50.000 6.01 0.00 0.00 2.08
651 662 2.696707 TGTTTTATCCGGCGTCCTATCT 59.303 45.455 6.01 0.00 0.00 1.98
652 663 3.243636 TGTTTTATCCGGCGTCCTATCTC 60.244 47.826 6.01 0.00 0.00 2.75
653 664 2.581216 TTATCCGGCGTCCTATCTCT 57.419 50.000 6.01 0.00 0.00 3.10
654 665 2.581216 TATCCGGCGTCCTATCTCTT 57.419 50.000 6.01 0.00 0.00 2.85
655 666 0.962489 ATCCGGCGTCCTATCTCTTG 59.038 55.000 6.01 0.00 0.00 3.02
662 673 3.869832 GGCGTCCTATCTCTTGTTTTACC 59.130 47.826 0.00 0.00 0.00 2.85
663 674 4.501071 GCGTCCTATCTCTTGTTTTACCA 58.499 43.478 0.00 0.00 0.00 3.25
667 678 7.262772 CGTCCTATCTCTTGTTTTACCACATA 58.737 38.462 0.00 0.00 0.00 2.29
685 696 7.370383 ACCACATAAACATTTGCTTCTTACTG 58.630 34.615 0.00 0.00 0.00 2.74
687 698 7.326789 CCACATAAACATTTGCTTCTTACTGTG 59.673 37.037 0.00 0.00 0.00 3.66
693 704 5.182001 ACATTTGCTTCTTACTGTGATGGTC 59.818 40.000 0.00 0.00 0.00 4.02
694 705 4.350368 TTGCTTCTTACTGTGATGGTCA 57.650 40.909 0.00 0.00 0.00 4.02
696 707 4.910195 TGCTTCTTACTGTGATGGTCATT 58.090 39.130 0.00 0.00 0.00 2.57
697 708 6.048732 TGCTTCTTACTGTGATGGTCATTA 57.951 37.500 0.00 0.00 0.00 1.90
698 709 6.653020 TGCTTCTTACTGTGATGGTCATTAT 58.347 36.000 0.00 0.00 0.00 1.28
699 710 6.539826 TGCTTCTTACTGTGATGGTCATTATG 59.460 38.462 0.00 0.00 0.00 1.90
700 711 6.512415 GCTTCTTACTGTGATGGTCATTATGC 60.512 42.308 0.00 0.00 0.00 3.14
701 712 6.239217 TCTTACTGTGATGGTCATTATGCT 57.761 37.500 0.00 0.00 0.00 3.79
703 714 4.767578 ACTGTGATGGTCATTATGCTCT 57.232 40.909 0.00 0.00 0.00 4.09
705 716 6.430962 ACTGTGATGGTCATTATGCTCTAT 57.569 37.500 0.00 0.00 0.00 1.98
710 732 6.815641 GTGATGGTCATTATGCTCTATAGTGG 59.184 42.308 0.00 0.00 31.78 4.00
714 736 6.498303 TGGTCATTATGCTCTATAGTGGATGT 59.502 38.462 16.37 5.11 31.78 3.06
718 740 8.309656 TCATTATGCTCTATAGTGGATGTCTTG 58.690 37.037 16.37 9.66 31.78 3.02
725 747 6.577103 TCTATAGTGGATGTCTTGCTGAAAG 58.423 40.000 0.00 0.00 37.22 2.62
744 766 8.336498 CTGAAAGCTGCATTTTATATTGAGTG 57.664 34.615 1.02 0.00 0.00 3.51
746 768 6.461110 AAGCTGCATTTTATATTGAGTGCT 57.539 33.333 1.02 0.00 33.95 4.40
752 774 5.973565 GCATTTTATATTGAGTGCTGTGGAC 59.026 40.000 0.00 0.00 0.00 4.02
762 784 1.525619 GTGCTGTGGACGTTACTTGTC 59.474 52.381 0.00 0.00 35.60 3.18
778 800 7.201393 CGTTACTTGTCTGCTCTGAAATTCTAG 60.201 40.741 0.00 0.00 0.00 2.43
784 806 3.999001 CTGCTCTGAAATTCTAGTGCACA 59.001 43.478 21.04 4.13 38.18 4.57
787 809 4.453819 GCTCTGAAATTCTAGTGCACAGTT 59.546 41.667 21.04 3.12 34.52 3.16
788 810 5.390356 GCTCTGAAATTCTAGTGCACAGTTC 60.390 44.000 21.04 13.33 34.52 3.01
789 811 5.858381 TCTGAAATTCTAGTGCACAGTTCT 58.142 37.500 21.04 0.00 0.00 3.01
790 812 6.993079 TCTGAAATTCTAGTGCACAGTTCTA 58.007 36.000 21.04 0.66 0.00 2.10
791 813 6.868864 TCTGAAATTCTAGTGCACAGTTCTAC 59.131 38.462 21.04 4.69 0.00 2.59
792 814 6.521162 TGAAATTCTAGTGCACAGTTCTACA 58.479 36.000 21.04 7.27 0.00 2.74
793 815 6.423905 TGAAATTCTAGTGCACAGTTCTACAC 59.576 38.462 21.04 4.03 0.00 2.90
799 831 4.261801 AGTGCACAGTTCTACACAACTTT 58.738 39.130 21.04 0.00 34.17 2.66
802 834 5.293569 GTGCACAGTTCTACACAACTTTACT 59.706 40.000 13.17 0.00 34.17 2.24
853 885 2.971330 TGAATTGTTTTCCATGTGCCCT 59.029 40.909 0.00 0.00 0.00 5.19
856 888 5.070981 TGAATTGTTTTCCATGTGCCCTTTA 59.929 36.000 0.00 0.00 0.00 1.85
892 924 3.940335 TCATGATGGACCTTCCTGGATA 58.060 45.455 11.23 0.00 37.46 2.59
900 932 4.540099 TGGACCTTCCTGGATATCACTTTT 59.460 41.667 4.83 0.00 37.46 2.27
1029 1061 1.331399 GGGAGAACGGGGAAGAGAGG 61.331 65.000 0.00 0.00 0.00 3.69
1517 1549 2.684943 TGATAATAAGGCCACCGAGGA 58.315 47.619 5.01 0.00 41.22 3.71
2092 2154 6.388435 ACGGGTCATAGTATGTCTTAACTC 57.612 41.667 9.94 0.00 0.00 3.01
2093 2155 6.127793 ACGGGTCATAGTATGTCTTAACTCT 58.872 40.000 9.94 0.00 0.00 3.24
2111 2173 3.018856 CTCTTTATTCTGCACATGGCCA 58.981 45.455 8.56 8.56 43.89 5.36
2262 2324 6.426980 TGCAGTTATGAATGCTTTCACTAG 57.573 37.500 16.45 7.26 44.36 2.57
2341 2403 0.611618 TGAATTCCGGTGGCAAGCAT 60.612 50.000 0.00 0.00 0.00 3.79
2523 2585 5.416013 AGAACCTTAAATTTGACCTGCTAGC 59.584 40.000 8.10 8.10 0.00 3.42
2539 2601 6.051717 CCTGCTAGCTGTAAAACATGACTAT 58.948 40.000 17.23 0.00 0.00 2.12
2648 2711 3.009363 TGAGGATTCATCAACTCCAAGCA 59.991 43.478 0.00 0.00 0.00 3.91
2701 2764 3.631144 TCAGCATCAAAGCACTTTTTCG 58.369 40.909 0.00 0.00 36.85 3.46
2724 2787 5.503683 CGATTGATCTTTGGAAGACTGCATC 60.504 44.000 0.00 0.00 41.01 3.91
2820 2883 6.461092 GCCAAACTGGTAAGCTTTAAGTTTCT 60.461 38.462 21.52 8.14 40.46 2.52
2871 2934 7.923888 TCTTTTGAGATATGTTTATGAGCTGC 58.076 34.615 0.00 0.00 0.00 5.25
3013 3076 1.005215 CTCCAGGGTTCTGCCAATTCT 59.995 52.381 0.00 0.00 39.61 2.40
3145 3208 8.422577 AAGAACAAACTAGAATAGGGCATTTT 57.577 30.769 0.00 0.00 44.97 1.82
3191 3262 6.489127 TTCTACCATTAAATGTTGACACGG 57.511 37.500 0.00 0.00 0.00 4.94
3441 3512 3.198872 GCATAACTCCTTGCTACACTCC 58.801 50.000 0.00 0.00 35.95 3.85
3671 3742 3.430098 GGAGCTGAACTCTGAGGTATGTG 60.430 52.174 9.85 0.00 45.48 3.21
3701 3772 5.716094 TGCTGAAGTTGAATGAATCCATTG 58.284 37.500 0.00 0.00 42.66 2.82
3704 3775 3.155093 AGTTGAATGAATCCATTGCGC 57.845 42.857 0.00 0.00 42.66 6.09
3886 3960 0.037326 TGTAGCGGAGAAAGTGGCAG 60.037 55.000 0.00 0.00 0.00 4.85
3960 4034 1.136147 GTACACCAGCGACGACGAT 59.864 57.895 12.29 0.40 42.66 3.73
4109 4183 2.145397 AGAGAAGTATGGTCGGAGCA 57.855 50.000 12.80 12.80 0.00 4.26
4195 4269 2.835764 AGTGTTAGGGGCGTGAAGAATA 59.164 45.455 0.00 0.00 0.00 1.75
4198 4272 3.139077 GTTAGGGGCGTGAAGAATATGG 58.861 50.000 0.00 0.00 0.00 2.74
4248 4322 1.445095 GATGATGGCTCCTCGCTGT 59.555 57.895 0.00 0.00 39.13 4.40
4377 4457 7.264373 ACTAGCATACATAGTGGAAAATTGC 57.736 36.000 0.00 0.00 32.27 3.56
4433 4513 9.772973 TGTAAAATATTAATGCGAGTATGGACT 57.227 29.630 0.00 0.00 39.20 3.85
4465 6322 0.701147 AAAGGCTGGAAGAAGGGGAG 59.299 55.000 0.00 0.00 34.07 4.30
4517 6374 4.717877 TCCTTGTGTGTTTGATCATGACT 58.282 39.130 0.00 0.00 0.00 3.41
4518 6375 4.516321 TCCTTGTGTGTTTGATCATGACTG 59.484 41.667 0.00 0.00 0.00 3.51
4519 6376 4.276678 CCTTGTGTGTTTGATCATGACTGT 59.723 41.667 0.00 0.00 0.00 3.55
4520 6377 5.469760 CCTTGTGTGTTTGATCATGACTGTA 59.530 40.000 0.00 0.00 0.00 2.74
4587 6454 1.597854 CGTGCCTGAGCTGTTTCCA 60.598 57.895 0.00 0.00 40.80 3.53
4608 6475 2.303311 ACTTTTCTAGTCTGGCTCCCAC 59.697 50.000 0.00 0.00 28.23 4.61
4616 6483 4.380945 TGGCTCCCACCATTGGCC 62.381 66.667 1.54 0.00 42.35 5.36
4669 6536 2.354403 GCTGCCCTTTTGCATTTCTGAT 60.354 45.455 0.00 0.00 41.16 2.90
4778 6710 1.299541 CTAGCAAAGCATGTACCGGG 58.700 55.000 6.32 0.00 0.00 5.73
4779 6711 0.906066 TAGCAAAGCATGTACCGGGA 59.094 50.000 6.32 0.00 0.00 5.14
4781 6713 0.958382 GCAAAGCATGTACCGGGACA 60.958 55.000 24.86 24.86 0.00 4.02
4782 6714 1.750193 CAAAGCATGTACCGGGACAT 58.250 50.000 27.40 27.40 40.78 3.06
4787 6719 3.317280 ATGTACCGGGACATGACCT 57.683 52.632 31.85 7.95 38.64 3.85
4818 6750 0.163788 GAACGGAGATGTTGTGTGCG 59.836 55.000 0.00 0.00 40.80 5.34
4840 6772 2.624838 CCAGTTCTTGTGATGGCAAAGT 59.375 45.455 0.00 0.00 0.00 2.66
4875 6811 0.391130 CAGCAACGGAGAAATCGGGA 60.391 55.000 0.00 0.00 0.00 5.14
4959 6895 2.107950 TAGCAAGTTCATGGTTCGGG 57.892 50.000 0.00 0.00 32.43 5.14
4960 6896 0.609131 AGCAAGTTCATGGTTCGGGG 60.609 55.000 0.00 0.00 0.00 5.73
4972 6908 1.173913 GTTCGGGGTTCCTTTGATGG 58.826 55.000 0.00 0.00 0.00 3.51
4978 6914 1.341089 GGGTTCCTTTGATGGACTCCC 60.341 57.143 0.00 0.00 40.59 4.30
4987 6923 2.108168 TGATGGACTCCCTCCGTAAAG 58.892 52.381 0.00 0.00 43.03 1.85
4991 6927 3.178865 TGGACTCCCTCCGTAAAGAAAT 58.821 45.455 0.00 0.00 43.03 2.17
4992 6928 4.355549 TGGACTCCCTCCGTAAAGAAATA 58.644 43.478 0.00 0.00 43.03 1.40
4993 6929 4.966805 TGGACTCCCTCCGTAAAGAAATAT 59.033 41.667 0.00 0.00 43.03 1.28
4994 6930 6.138263 TGGACTCCCTCCGTAAAGAAATATA 58.862 40.000 0.00 0.00 43.03 0.86
4995 6931 6.612456 TGGACTCCCTCCGTAAAGAAATATAA 59.388 38.462 0.00 0.00 43.03 0.98
4996 6932 7.153315 GGACTCCCTCCGTAAAGAAATATAAG 58.847 42.308 0.00 0.00 0.00 1.73
4997 6933 7.015001 GGACTCCCTCCGTAAAGAAATATAAGA 59.985 40.741 0.00 0.00 0.00 2.10
4998 6934 8.493787 ACTCCCTCCGTAAAGAAATATAAGAT 57.506 34.615 0.00 0.00 0.00 2.40
4999 6935 8.586744 ACTCCCTCCGTAAAGAAATATAAGATC 58.413 37.037 0.00 0.00 0.00 2.75
5000 6936 7.600065 TCCCTCCGTAAAGAAATATAAGATCG 58.400 38.462 0.00 0.00 0.00 3.69
5001 6937 7.232127 TCCCTCCGTAAAGAAATATAAGATCGT 59.768 37.037 0.00 0.00 0.00 3.73
5002 6938 8.517878 CCCTCCGTAAAGAAATATAAGATCGTA 58.482 37.037 0.00 0.00 0.00 3.43
5003 6939 9.557338 CCTCCGTAAAGAAATATAAGATCGTAG 57.443 37.037 0.00 0.00 0.00 3.51
5004 6940 8.961294 TCCGTAAAGAAATATAAGATCGTAGC 57.039 34.615 0.00 0.00 0.00 3.58
5005 6941 8.570488 TCCGTAAAGAAATATAAGATCGTAGCA 58.430 33.333 0.00 0.00 0.00 3.49
5006 6942 9.188588 CCGTAAAGAAATATAAGATCGTAGCAA 57.811 33.333 0.00 0.00 0.00 3.91
5021 6957 9.862371 AGATCGTAGCAATCCTAGTATTTTATG 57.138 33.333 0.00 0.00 0.00 1.90
5022 6958 9.640963 GATCGTAGCAATCCTAGTATTTTATGT 57.359 33.333 0.00 0.00 0.00 2.29
5023 6959 9.998106 ATCGTAGCAATCCTAGTATTTTATGTT 57.002 29.630 0.00 0.00 0.00 2.71
5024 6960 9.826574 TCGTAGCAATCCTAGTATTTTATGTTT 57.173 29.630 0.00 0.00 0.00 2.83
5032 6968 8.259049 TCCTAGTATTTTATGTTTTGTCACCG 57.741 34.615 0.00 0.00 0.00 4.94
5033 6969 7.334921 TCCTAGTATTTTATGTTTTGTCACCGG 59.665 37.037 0.00 0.00 0.00 5.28
5034 6970 5.705902 AGTATTTTATGTTTTGTCACCGGC 58.294 37.500 0.00 0.00 0.00 6.13
5035 6971 3.372660 TTTTATGTTTTGTCACCGGCC 57.627 42.857 0.00 0.00 0.00 6.13
5036 6972 1.249407 TTATGTTTTGTCACCGGCCC 58.751 50.000 0.00 0.00 0.00 5.80
5037 6973 0.956410 TATGTTTTGTCACCGGCCCG 60.956 55.000 0.00 0.00 0.00 6.13
5038 6974 2.903350 GTTTTGTCACCGGCCCGT 60.903 61.111 0.00 0.00 0.00 5.28
5039 6975 1.597578 GTTTTGTCACCGGCCCGTA 60.598 57.895 0.00 0.00 0.00 4.02
5040 6976 1.597578 TTTTGTCACCGGCCCGTAC 60.598 57.895 0.00 0.00 0.00 3.67
5041 6977 3.862394 TTTGTCACCGGCCCGTACG 62.862 63.158 8.69 8.69 0.00 3.67
5043 6979 4.362476 GTCACCGGCCCGTACGTT 62.362 66.667 15.21 0.00 0.00 3.99
5044 6980 3.614698 TCACCGGCCCGTACGTTT 61.615 61.111 15.21 0.00 0.00 3.60
5045 6981 2.665854 CACCGGCCCGTACGTTTT 60.666 61.111 15.21 0.00 0.00 2.43
5046 6982 2.357396 ACCGGCCCGTACGTTTTC 60.357 61.111 15.21 0.00 0.00 2.29
5047 6983 3.120385 CCGGCCCGTACGTTTTCC 61.120 66.667 15.21 8.22 0.00 3.13
5048 6984 2.047939 CGGCCCGTACGTTTTCCT 60.048 61.111 15.21 0.00 0.00 3.36
5049 6985 1.668793 CGGCCCGTACGTTTTCCTT 60.669 57.895 15.21 0.00 0.00 3.36
5050 6986 1.629345 CGGCCCGTACGTTTTCCTTC 61.629 60.000 15.21 0.00 0.00 3.46
5051 6987 1.300971 GGCCCGTACGTTTTCCTTCC 61.301 60.000 15.21 0.00 0.00 3.46
5052 6988 1.300971 GCCCGTACGTTTTCCTTCCC 61.301 60.000 15.21 0.00 0.00 3.97
5053 6989 0.322648 CCCGTACGTTTTCCTTCCCT 59.677 55.000 15.21 0.00 0.00 4.20
5054 6990 1.271001 CCCGTACGTTTTCCTTCCCTT 60.271 52.381 15.21 0.00 0.00 3.95
5055 6991 2.071540 CCGTACGTTTTCCTTCCCTTC 58.928 52.381 15.21 0.00 0.00 3.46
5056 6992 2.071540 CGTACGTTTTCCTTCCCTTCC 58.928 52.381 7.22 0.00 0.00 3.46
5057 6993 2.430465 GTACGTTTTCCTTCCCTTCCC 58.570 52.381 0.00 0.00 0.00 3.97
5058 6994 0.111832 ACGTTTTCCTTCCCTTCCCC 59.888 55.000 0.00 0.00 0.00 4.81
5059 6995 0.404426 CGTTTTCCTTCCCTTCCCCT 59.596 55.000 0.00 0.00 0.00 4.79
5060 6996 1.613520 CGTTTTCCTTCCCTTCCCCTC 60.614 57.143 0.00 0.00 0.00 4.30
5061 6997 0.696501 TTTTCCTTCCCTTCCCCTCG 59.303 55.000 0.00 0.00 0.00 4.63
5062 6998 0.475048 TTTCCTTCCCTTCCCCTCGT 60.475 55.000 0.00 0.00 0.00 4.18
5063 6999 0.414629 TTCCTTCCCTTCCCCTCGTA 59.585 55.000 0.00 0.00 0.00 3.43
5064 7000 0.414629 TCCTTCCCTTCCCCTCGTAA 59.585 55.000 0.00 0.00 0.00 3.18
5065 7001 0.540454 CCTTCCCTTCCCCTCGTAAC 59.460 60.000 0.00 0.00 0.00 2.50
5066 7002 0.540454 CTTCCCTTCCCCTCGTAACC 59.460 60.000 0.00 0.00 0.00 2.85
5067 7003 1.259840 TTCCCTTCCCCTCGTAACCG 61.260 60.000 0.00 0.00 0.00 4.44
5068 7004 2.728435 CCCTTCCCCTCGTAACCGG 61.728 68.421 0.00 0.00 33.95 5.28
5069 7005 2.186125 CTTCCCCTCGTAACCGGC 59.814 66.667 0.00 0.00 33.95 6.13
5070 7006 3.711541 CTTCCCCTCGTAACCGGCG 62.712 68.421 0.00 0.00 33.95 6.46
5074 7010 4.446413 CCTCGTAACCGGCGGCTT 62.446 66.667 28.71 20.95 33.95 4.35
5075 7011 2.884207 CTCGTAACCGGCGGCTTC 60.884 66.667 28.71 11.38 33.95 3.86
5076 7012 4.781959 TCGTAACCGGCGGCTTCG 62.782 66.667 28.71 23.83 33.95 3.79
5085 7021 3.050275 GCGGCTTCGGCAAACTCT 61.050 61.111 0.00 0.00 43.96 3.24
5086 7022 2.617274 GCGGCTTCGGCAAACTCTT 61.617 57.895 0.00 0.00 43.96 2.85
5087 7023 1.949257 CGGCTTCGGCAAACTCTTT 59.051 52.632 0.00 0.00 43.96 2.52
5088 7024 0.110192 CGGCTTCGGCAAACTCTTTC 60.110 55.000 0.00 0.00 43.96 2.62
5089 7025 0.241213 GGCTTCGGCAAACTCTTTCC 59.759 55.000 0.00 0.00 43.96 3.13
5090 7026 0.241213 GCTTCGGCAAACTCTTTCCC 59.759 55.000 0.00 0.00 41.33 3.97
5091 7027 1.897560 CTTCGGCAAACTCTTTCCCT 58.102 50.000 0.00 0.00 0.00 4.20
5092 7028 1.807142 CTTCGGCAAACTCTTTCCCTC 59.193 52.381 0.00 0.00 0.00 4.30
5093 7029 0.036306 TCGGCAAACTCTTTCCCTCC 59.964 55.000 0.00 0.00 0.00 4.30
5094 7030 0.250727 CGGCAAACTCTTTCCCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
5095 7031 1.539157 GGCAAACTCTTTCCCTCCAG 58.461 55.000 0.00 0.00 0.00 3.86
5096 7032 1.539157 GCAAACTCTTTCCCTCCAGG 58.461 55.000 0.00 0.00 0.00 4.45
5097 7033 1.539157 CAAACTCTTTCCCTCCAGGC 58.461 55.000 0.00 0.00 34.51 4.85
5098 7034 1.074566 CAAACTCTTTCCCTCCAGGCT 59.925 52.381 0.00 0.00 34.51 4.58
5099 7035 0.988063 AACTCTTTCCCTCCAGGCTC 59.012 55.000 0.00 0.00 34.51 4.70
5100 7036 0.912006 ACTCTTTCCCTCCAGGCTCC 60.912 60.000 0.00 0.00 34.51 4.70
5101 7037 1.965754 CTCTTTCCCTCCAGGCTCCG 61.966 65.000 0.00 0.00 34.51 4.63
5102 7038 3.689002 CTTTCCCTCCAGGCTCCGC 62.689 68.421 0.00 0.00 34.51 5.54
5113 7049 4.954933 GCTCCGCCAATTAGTCCA 57.045 55.556 0.00 0.00 0.00 4.02
5114 7050 3.403936 GCTCCGCCAATTAGTCCAT 57.596 52.632 0.00 0.00 0.00 3.41
5115 7051 0.947244 GCTCCGCCAATTAGTCCATG 59.053 55.000 0.00 0.00 0.00 3.66
5116 7052 1.597742 CTCCGCCAATTAGTCCATGG 58.402 55.000 4.97 4.97 37.29 3.66
5117 7053 1.140852 CTCCGCCAATTAGTCCATGGA 59.859 52.381 11.44 11.44 36.27 3.41
5118 7054 1.774254 TCCGCCAATTAGTCCATGGAT 59.226 47.619 19.62 9.69 36.27 3.41
5119 7055 2.174639 TCCGCCAATTAGTCCATGGATT 59.825 45.455 19.62 17.06 36.27 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.525077 GCGGACACCAACAGAACCA 60.525 57.895 0.00 0.00 0.00 3.67
75 76 6.837992 TGACTAACTGAATTTTACGAATGGC 58.162 36.000 0.00 0.00 0.00 4.40
103 104 8.729805 AGAATGTCCAGAGAAAAATATCAGAC 57.270 34.615 0.00 0.00 0.00 3.51
107 108 9.780413 GTTCAAGAATGTCCAGAGAAAAATATC 57.220 33.333 0.00 0.00 0.00 1.63
115 121 5.815233 AGAAGTTCAAGAATGTCCAGAGA 57.185 39.130 5.50 0.00 0.00 3.10
117 123 4.991056 CGAAGAAGTTCAAGAATGTCCAGA 59.009 41.667 5.50 0.00 32.36 3.86
175 181 1.202313 GCAGTACTCACTCCGATCCAC 60.202 57.143 0.00 0.00 30.46 4.02
187 193 0.514691 GCAAGTGCAGTGCAGTACTC 59.485 55.000 25.30 13.36 41.77 2.59
188 194 0.179048 TGCAAGTGCAGTGCAGTACT 60.179 50.000 25.30 13.20 46.76 2.73
189 195 2.320215 TGCAAGTGCAGTGCAGTAC 58.680 52.632 25.30 19.79 46.76 2.73
190 196 4.874528 TGCAAGTGCAGTGCAGTA 57.125 50.000 25.30 7.85 46.76 2.74
229 235 0.682855 GAATTTCCCATCACCGGGCA 60.683 55.000 6.32 0.00 46.92 5.36
298 308 0.519519 CAAATGTAAACTCGGCGCCA 59.480 50.000 28.98 12.94 0.00 5.69
301 311 2.737783 TGTACCAAATGTAAACTCGGCG 59.262 45.455 0.00 0.00 0.00 6.46
337 347 2.918712 AGCTGTACTGCTGAAACTGT 57.081 45.000 24.53 0.00 42.33 3.55
339 349 3.313526 CACAAAGCTGTACTGCTGAAACT 59.686 43.478 25.62 8.84 43.24 2.66
341 351 3.278574 ACACAAAGCTGTACTGCTGAAA 58.721 40.909 25.62 0.00 43.24 2.69
343 353 2.483876 GACACAAAGCTGTACTGCTGA 58.516 47.619 25.62 0.00 43.24 4.26
344 354 1.532868 GGACACAAAGCTGTACTGCTG 59.467 52.381 25.62 17.74 43.24 4.41
345 355 1.543429 GGGACACAAAGCTGTACTGCT 60.543 52.381 20.37 20.37 46.40 4.24
346 356 0.875059 GGGACACAAAGCTGTACTGC 59.125 55.000 16.28 16.28 33.22 4.40
351 361 1.529244 GCCAGGGACACAAAGCTGT 60.529 57.895 0.00 0.00 35.63 4.40
352 362 2.620112 CGCCAGGGACACAAAGCTG 61.620 63.158 0.00 0.00 0.00 4.24
353 363 2.281761 CGCCAGGGACACAAAGCT 60.282 61.111 0.00 0.00 0.00 3.74
355 365 1.898574 AAGCGCCAGGGACACAAAG 60.899 57.895 2.29 0.00 0.00 2.77
357 367 2.594303 CAAGCGCCAGGGACACAA 60.594 61.111 2.29 0.00 0.00 3.33
358 368 4.641645 CCAAGCGCCAGGGACACA 62.642 66.667 2.29 0.00 0.00 3.72
364 374 3.944250 ATTGGACCCAAGCGCCAGG 62.944 63.158 2.29 6.20 39.47 4.45
365 375 1.978617 AATTGGACCCAAGCGCCAG 60.979 57.895 2.29 0.00 39.47 4.85
366 376 2.117206 AATTGGACCCAAGCGCCA 59.883 55.556 2.29 0.00 39.47 5.69
367 377 2.573340 CAATTGGACCCAAGCGCC 59.427 61.111 2.29 0.00 39.47 6.53
368 378 2.573340 CCAATTGGACCCAAGCGC 59.427 61.111 20.50 0.00 39.47 5.92
369 379 1.304052 TCCCAATTGGACCCAAGCG 60.304 57.895 26.60 6.41 38.61 4.68
370 380 0.251787 ACTCCCAATTGGACCCAAGC 60.252 55.000 26.60 0.00 38.61 4.01
371 381 1.895131 CAACTCCCAATTGGACCCAAG 59.105 52.381 26.60 15.55 38.61 3.61
479 489 2.450476 GTGCAATTCACTTGAGGGGAT 58.550 47.619 0.00 0.00 42.38 3.85
515 526 4.460382 CAGCAACAAGAGAATTGGGTACAT 59.540 41.667 0.00 0.00 0.00 2.29
589 600 2.513753 CCTCGAGATCTGGACAGCTAT 58.486 52.381 15.71 0.00 0.00 2.97
625 636 2.273557 GACGCCGGATAAAACAGCTAA 58.726 47.619 5.05 0.00 0.00 3.09
635 646 2.160205 CAAGAGATAGGACGCCGGATA 58.840 52.381 5.05 0.00 0.00 2.59
643 654 9.444600 TTTATGTGGTAAAACAAGAGATAGGAC 57.555 33.333 0.00 0.00 32.81 3.85
650 661 8.487176 GCAAATGTTTATGTGGTAAAACAAGAG 58.513 33.333 4.90 0.45 45.69 2.85
651 662 8.200792 AGCAAATGTTTATGTGGTAAAACAAGA 58.799 29.630 4.90 0.00 45.69 3.02
652 663 8.364129 AGCAAATGTTTATGTGGTAAAACAAG 57.636 30.769 4.90 1.03 45.69 3.16
653 664 8.723942 AAGCAAATGTTTATGTGGTAAAACAA 57.276 26.923 4.90 0.00 45.69 2.83
654 665 8.200792 AGAAGCAAATGTTTATGTGGTAAAACA 58.799 29.630 3.40 3.40 46.37 2.83
655 666 8.587952 AGAAGCAAATGTTTATGTGGTAAAAC 57.412 30.769 0.00 0.00 31.14 2.43
662 673 8.075574 TCACAGTAAGAAGCAAATGTTTATGTG 58.924 33.333 0.00 0.00 34.58 3.21
663 674 8.165239 TCACAGTAAGAAGCAAATGTTTATGT 57.835 30.769 0.00 0.00 0.00 2.29
667 678 6.040842 ACCATCACAGTAAGAAGCAAATGTTT 59.959 34.615 0.00 0.00 0.00 2.83
685 696 6.815641 CCACTATAGAGCATAATGACCATCAC 59.184 42.308 6.78 0.00 0.00 3.06
687 698 7.175347 TCCACTATAGAGCATAATGACCATC 57.825 40.000 6.78 0.00 0.00 3.51
693 704 7.064371 GCAAGACATCCACTATAGAGCATAATG 59.936 40.741 6.78 4.21 0.00 1.90
694 705 7.038445 AGCAAGACATCCACTATAGAGCATAAT 60.038 37.037 6.78 0.00 0.00 1.28
696 707 5.777223 AGCAAGACATCCACTATAGAGCATA 59.223 40.000 6.78 0.00 0.00 3.14
697 708 4.592351 AGCAAGACATCCACTATAGAGCAT 59.408 41.667 6.78 0.00 0.00 3.79
698 709 3.963374 AGCAAGACATCCACTATAGAGCA 59.037 43.478 6.78 0.00 0.00 4.26
699 710 4.038522 TCAGCAAGACATCCACTATAGAGC 59.961 45.833 6.78 0.00 0.00 4.09
700 711 5.781210 TCAGCAAGACATCCACTATAGAG 57.219 43.478 6.78 0.00 0.00 2.43
701 712 6.544928 TTTCAGCAAGACATCCACTATAGA 57.455 37.500 6.78 0.00 0.00 1.98
703 714 5.104776 AGCTTTCAGCAAGACATCCACTATA 60.105 40.000 0.00 0.00 45.56 1.31
705 716 3.008375 AGCTTTCAGCAAGACATCCACTA 59.992 43.478 0.00 0.00 45.56 2.74
710 732 1.538512 TGCAGCTTTCAGCAAGACATC 59.461 47.619 0.00 0.00 45.56 3.06
714 736 3.738830 AAAATGCAGCTTTCAGCAAGA 57.261 38.095 0.07 0.00 45.56 3.02
718 740 6.976925 ACTCAATATAAAATGCAGCTTTCAGC 59.023 34.615 0.00 0.00 42.84 4.26
725 747 5.457799 CACAGCACTCAATATAAAATGCAGC 59.542 40.000 0.00 0.00 35.51 5.25
737 759 2.037251 AGTAACGTCCACAGCACTCAAT 59.963 45.455 0.00 0.00 0.00 2.57
744 766 1.792949 CAGACAAGTAACGTCCACAGC 59.207 52.381 0.00 0.00 33.70 4.40
746 768 1.411246 AGCAGACAAGTAACGTCCACA 59.589 47.619 0.00 0.00 33.70 4.17
752 774 5.406780 AGAATTTCAGAGCAGACAAGTAACG 59.593 40.000 0.00 0.00 0.00 3.18
762 784 3.999001 TGTGCACTAGAATTTCAGAGCAG 59.001 43.478 19.41 4.99 38.72 4.24
778 800 4.616181 AAAGTTGTGTAGAACTGTGCAC 57.384 40.909 10.75 10.75 36.28 4.57
827 859 6.925165 GGGCACATGGAAAACAATTCATATAG 59.075 38.462 0.00 0.00 0.00 1.31
828 860 6.610830 AGGGCACATGGAAAACAATTCATATA 59.389 34.615 0.00 0.00 0.00 0.86
829 861 5.426185 AGGGCACATGGAAAACAATTCATAT 59.574 36.000 0.00 0.00 0.00 1.78
830 862 4.776837 AGGGCACATGGAAAACAATTCATA 59.223 37.500 0.00 0.00 0.00 2.15
831 863 3.583966 AGGGCACATGGAAAACAATTCAT 59.416 39.130 0.00 0.00 0.00 2.57
832 864 2.971330 AGGGCACATGGAAAACAATTCA 59.029 40.909 0.00 0.00 0.00 2.57
833 865 3.683365 AGGGCACATGGAAAACAATTC 57.317 42.857 0.00 0.00 0.00 2.17
834 866 4.436113 AAAGGGCACATGGAAAACAATT 57.564 36.364 0.00 0.00 0.00 2.32
835 867 4.262851 GGTAAAGGGCACATGGAAAACAAT 60.263 41.667 0.00 0.00 0.00 2.71
836 868 3.070302 GGTAAAGGGCACATGGAAAACAA 59.930 43.478 0.00 0.00 0.00 2.83
837 869 2.630580 GGTAAAGGGCACATGGAAAACA 59.369 45.455 0.00 0.00 0.00 2.83
853 885 7.093684 CCATCATGATGATTATGCCATGGTAAA 60.094 37.037 32.71 6.75 41.20 2.01
856 888 4.709886 CCATCATGATGATTATGCCATGGT 59.290 41.667 32.71 0.00 41.20 3.55
892 924 8.174733 CCAATAGGCATGATAGAAAAAGTGAT 57.825 34.615 0.00 0.00 0.00 3.06
1029 1061 4.701651 TCCACATCAGTTGAATGGTCATTC 59.298 41.667 14.75 14.75 45.55 2.67
1517 1549 2.915349 CCTTATCATCAGCAGCTGTGT 58.085 47.619 22.10 9.59 32.61 3.72
2092 2154 3.382227 TCATGGCCATGTGCAGAATAAAG 59.618 43.478 38.18 14.19 43.89 1.85
2093 2155 3.363627 TCATGGCCATGTGCAGAATAAA 58.636 40.909 38.18 17.48 43.89 1.40
2154 2216 7.068962 TCGATAACCAGAATGTCAACCTACATA 59.931 37.037 0.00 0.00 39.16 2.29
2341 2403 4.474394 ACTGCATGATAGTAGGTCTAGCA 58.526 43.478 0.00 0.00 46.77 3.49
2560 2622 6.609237 ACCGATCAGAATATTGACAACATG 57.391 37.500 0.00 0.00 0.00 3.21
2561 2623 8.908786 AATACCGATCAGAATATTGACAACAT 57.091 30.769 0.00 0.00 0.00 2.71
2562 2624 8.731275 AAATACCGATCAGAATATTGACAACA 57.269 30.769 0.00 0.00 0.00 3.33
2563 2625 9.046296 AGAAATACCGATCAGAATATTGACAAC 57.954 33.333 0.00 0.00 0.00 3.32
2564 2626 9.613428 AAGAAATACCGATCAGAATATTGACAA 57.387 29.630 0.00 0.00 0.00 3.18
2648 2711 3.732048 ATGTCCTAACGGTTTCCCAAT 57.268 42.857 0.00 0.00 0.00 3.16
2701 2764 5.589452 AGATGCAGTCTTCCAAAGATCAATC 59.411 40.000 0.00 0.00 40.18 2.67
2854 2917 6.857777 AACAGAGCAGCTCATAAACATATC 57.142 37.500 24.64 0.00 32.06 1.63
2857 2920 6.351711 TGATAACAGAGCAGCTCATAAACAT 58.648 36.000 24.64 9.22 32.06 2.71
3013 3076 2.819608 CCAAAGCTTAAGTTGCCAGCTA 59.180 45.455 0.00 0.00 43.28 3.32
3145 3208 4.656100 TTGTTTGGAAGGAGGATCATCA 57.344 40.909 9.94 0.00 36.25 3.07
3191 3262 1.616994 CCAACCTGGGGAGTCATTTCC 60.617 57.143 0.00 0.00 32.67 3.13
3410 3481 1.076332 GGAGTTATGCACGGACACAC 58.924 55.000 0.00 0.00 0.00 3.82
3495 3566 7.387122 CCACATCTGACAGTTCCATATAAGATG 59.613 40.741 1.59 7.58 43.37 2.90
3671 3742 3.750130 TCATTCAACTTCAGCAAGAGAGC 59.250 43.478 0.00 0.00 33.34 4.09
3960 4034 1.076923 GGAGCCTAGGTCGTCCAGA 60.077 63.158 11.31 0.00 35.89 3.86
4109 4183 2.507102 CGCTCGCTCAATCACGGT 60.507 61.111 0.00 0.00 0.00 4.83
4218 4292 3.563223 AGCCATCATCCCTCTTTGATTG 58.437 45.455 0.00 0.00 30.24 2.67
4248 4322 0.833949 GGGGGCAAAGGAAACAACAA 59.166 50.000 0.00 0.00 0.00 2.83
4326 4401 8.348507 ACATGAGAAGAAGAAAAAGCAACTAAG 58.651 33.333 0.00 0.00 0.00 2.18
4377 4457 4.009675 TCGAATTCACCATCCTTTCCTTG 58.990 43.478 6.22 0.00 0.00 3.61
4433 4513 3.136809 TCCAGCCTTTACTTACACCACAA 59.863 43.478 0.00 0.00 0.00 3.33
4435 4515 3.412237 TCCAGCCTTTACTTACACCAC 57.588 47.619 0.00 0.00 0.00 4.16
4465 6322 1.348036 GTACCCAGGCCAGGATCATAC 59.652 57.143 17.38 8.69 0.00 2.39
4517 6374 4.142790 GTCGGGGAAGAGAGATACATACA 58.857 47.826 0.00 0.00 0.00 2.29
4518 6375 4.142790 TGTCGGGGAAGAGAGATACATAC 58.857 47.826 0.00 0.00 0.00 2.39
4519 6376 4.141228 ACTGTCGGGGAAGAGAGATACATA 60.141 45.833 0.00 0.00 35.38 2.29
4520 6377 3.226777 CTGTCGGGGAAGAGAGATACAT 58.773 50.000 0.00 0.00 33.85 2.29
4587 6454 2.303311 GTGGGAGCCAGACTAGAAAAGT 59.697 50.000 0.00 0.00 42.80 2.66
4608 6475 3.443045 GGACAGCACGGCCAATGG 61.443 66.667 2.24 0.00 0.00 3.16
4669 6536 0.251297 CCTGCTGGTGTTCATTCCCA 60.251 55.000 0.51 0.00 0.00 4.37
4778 6710 2.093973 CAGTCCAGGTACAGGTCATGTC 60.094 54.545 0.00 0.00 42.70 3.06
4779 6711 1.902508 CAGTCCAGGTACAGGTCATGT 59.097 52.381 0.00 0.00 46.45 3.21
4781 6713 2.567615 GTTCAGTCCAGGTACAGGTCAT 59.432 50.000 0.00 0.00 35.97 3.06
4782 6714 1.968493 GTTCAGTCCAGGTACAGGTCA 59.032 52.381 0.00 0.00 35.97 4.02
4787 6719 1.202964 TCTCCGTTCAGTCCAGGTACA 60.203 52.381 0.00 0.00 0.00 2.90
4818 6750 0.961019 TTGCCATCACAAGAACTGGC 59.039 50.000 5.48 5.48 45.86 4.85
4840 6772 4.560743 TGCCAGCGTGCCAACTGA 62.561 61.111 0.00 0.00 35.90 3.41
4875 6811 4.479993 GGCTGCATCGGTCCTGCT 62.480 66.667 0.50 0.00 40.34 4.24
4959 6895 1.636003 AGGGAGTCCATCAAAGGAACC 59.364 52.381 12.30 0.00 39.92 3.62
4960 6896 2.356227 GGAGGGAGTCCATCAAAGGAAC 60.356 54.545 24.40 2.36 46.10 3.62
4972 6908 7.949434 TCTTATATTTCTTTACGGAGGGAGTC 58.051 38.462 0.00 0.00 0.00 3.36
4978 6914 9.063739 GCTACGATCTTATATTTCTTTACGGAG 57.936 37.037 0.00 0.00 0.00 4.63
4995 6931 9.862371 CATAAAATACTAGGATTGCTACGATCT 57.138 33.333 0.00 0.00 0.00 2.75
4996 6932 9.640963 ACATAAAATACTAGGATTGCTACGATC 57.359 33.333 0.00 0.00 0.00 3.69
4997 6933 9.998106 AACATAAAATACTAGGATTGCTACGAT 57.002 29.630 0.00 0.00 0.00 3.73
4998 6934 9.826574 AAACATAAAATACTAGGATTGCTACGA 57.173 29.630 0.00 0.00 0.00 3.43
5006 6942 8.889717 CGGTGACAAAACATAAAATACTAGGAT 58.110 33.333 0.00 0.00 0.00 3.24
5007 6943 7.334921 CCGGTGACAAAACATAAAATACTAGGA 59.665 37.037 0.00 0.00 0.00 2.94
5008 6944 7.469260 CCGGTGACAAAACATAAAATACTAGG 58.531 38.462 0.00 0.00 0.00 3.02
5009 6945 6.964934 GCCGGTGACAAAACATAAAATACTAG 59.035 38.462 1.90 0.00 0.00 2.57
5010 6946 6.127952 GGCCGGTGACAAAACATAAAATACTA 60.128 38.462 1.90 0.00 0.00 1.82
5011 6947 5.336134 GGCCGGTGACAAAACATAAAATACT 60.336 40.000 1.90 0.00 0.00 2.12
5012 6948 4.860352 GGCCGGTGACAAAACATAAAATAC 59.140 41.667 1.90 0.00 0.00 1.89
5013 6949 4.082136 GGGCCGGTGACAAAACATAAAATA 60.082 41.667 1.90 0.00 0.00 1.40
5014 6950 3.306433 GGGCCGGTGACAAAACATAAAAT 60.306 43.478 1.90 0.00 0.00 1.82
5015 6951 2.036089 GGGCCGGTGACAAAACATAAAA 59.964 45.455 1.90 0.00 0.00 1.52
5016 6952 1.614413 GGGCCGGTGACAAAACATAAA 59.386 47.619 1.90 0.00 0.00 1.40
5017 6953 1.249407 GGGCCGGTGACAAAACATAA 58.751 50.000 1.90 0.00 0.00 1.90
5018 6954 0.956410 CGGGCCGGTGACAAAACATA 60.956 55.000 20.56 0.00 0.00 2.29
5019 6955 2.265182 CGGGCCGGTGACAAAACAT 61.265 57.895 20.56 0.00 0.00 2.71
5020 6956 2.321263 TACGGGCCGGTGACAAAACA 62.321 55.000 31.78 0.00 0.00 2.83
5021 6957 1.597578 TACGGGCCGGTGACAAAAC 60.598 57.895 31.78 0.00 0.00 2.43
5022 6958 1.597578 GTACGGGCCGGTGACAAAA 60.598 57.895 31.78 1.48 0.00 2.44
5023 6959 2.030862 GTACGGGCCGGTGACAAA 59.969 61.111 31.78 2.26 0.00 2.83
5024 6960 4.360964 CGTACGGGCCGGTGACAA 62.361 66.667 31.78 2.67 0.00 3.18
5026 6962 3.864160 AAACGTACGGGCCGGTGAC 62.864 63.158 31.78 22.44 0.00 3.67
5027 6963 3.162505 AAAACGTACGGGCCGGTGA 62.163 57.895 31.78 12.45 0.00 4.02
5028 6964 2.665854 AAAACGTACGGGCCGGTG 60.666 61.111 31.78 20.91 0.00 4.94
5029 6965 2.357396 GAAAACGTACGGGCCGGT 60.357 61.111 31.78 20.77 0.00 5.28
5030 6966 3.120385 GGAAAACGTACGGGCCGG 61.120 66.667 31.78 15.34 0.00 6.13
5031 6967 1.629345 GAAGGAAAACGTACGGGCCG 61.629 60.000 27.06 27.06 0.00 6.13
5032 6968 1.300971 GGAAGGAAAACGTACGGGCC 61.301 60.000 21.06 14.15 0.00 5.80
5033 6969 1.300971 GGGAAGGAAAACGTACGGGC 61.301 60.000 21.06 5.34 0.00 6.13
5034 6970 0.322648 AGGGAAGGAAAACGTACGGG 59.677 55.000 21.06 0.00 0.00 5.28
5035 6971 2.071540 GAAGGGAAGGAAAACGTACGG 58.928 52.381 21.06 1.43 0.00 4.02
5036 6972 2.071540 GGAAGGGAAGGAAAACGTACG 58.928 52.381 15.01 15.01 0.00 3.67
5037 6973 2.430465 GGGAAGGGAAGGAAAACGTAC 58.570 52.381 0.00 0.00 0.00 3.67
5038 6974 1.352017 GGGGAAGGGAAGGAAAACGTA 59.648 52.381 0.00 0.00 0.00 3.57
5039 6975 0.111832 GGGGAAGGGAAGGAAAACGT 59.888 55.000 0.00 0.00 0.00 3.99
5040 6976 0.404426 AGGGGAAGGGAAGGAAAACG 59.596 55.000 0.00 0.00 0.00 3.60
5041 6977 1.613520 CGAGGGGAAGGGAAGGAAAAC 60.614 57.143 0.00 0.00 0.00 2.43
5042 6978 0.696501 CGAGGGGAAGGGAAGGAAAA 59.303 55.000 0.00 0.00 0.00 2.29
5043 6979 0.475048 ACGAGGGGAAGGGAAGGAAA 60.475 55.000 0.00 0.00 0.00 3.13
5044 6980 0.414629 TACGAGGGGAAGGGAAGGAA 59.585 55.000 0.00 0.00 0.00 3.36
5045 6981 0.414629 TTACGAGGGGAAGGGAAGGA 59.585 55.000 0.00 0.00 0.00 3.36
5046 6982 0.540454 GTTACGAGGGGAAGGGAAGG 59.460 60.000 0.00 0.00 0.00 3.46
5047 6983 0.540454 GGTTACGAGGGGAAGGGAAG 59.460 60.000 0.00 0.00 0.00 3.46
5048 6984 1.259840 CGGTTACGAGGGGAAGGGAA 61.260 60.000 0.00 0.00 44.60 3.97
5049 6985 1.683365 CGGTTACGAGGGGAAGGGA 60.683 63.158 0.00 0.00 44.60 4.20
5050 6986 2.728435 CCGGTTACGAGGGGAAGGG 61.728 68.421 0.00 0.00 44.60 3.95
5051 6987 2.897972 CCGGTTACGAGGGGAAGG 59.102 66.667 0.00 0.00 44.60 3.46
5052 6988 2.186125 GCCGGTTACGAGGGGAAG 59.814 66.667 1.90 0.00 44.60 3.46
5053 6989 3.762247 CGCCGGTTACGAGGGGAA 61.762 66.667 1.90 0.00 44.60 3.97
5057 6993 4.446413 AAGCCGCCGGTTACGAGG 62.446 66.667 4.45 0.00 44.60 4.63
5058 6994 2.884207 GAAGCCGCCGGTTACGAG 60.884 66.667 4.45 0.00 44.60 4.18
5059 6995 4.781959 CGAAGCCGCCGGTTACGA 62.782 66.667 4.45 0.00 44.60 3.43
5067 7003 4.103103 GAGTTTGCCGAAGCCGCC 62.103 66.667 0.00 0.00 38.69 6.13
5068 7004 2.130073 AAAGAGTTTGCCGAAGCCGC 62.130 55.000 0.00 0.00 38.69 6.53
5069 7005 0.110192 GAAAGAGTTTGCCGAAGCCG 60.110 55.000 0.00 0.00 38.69 5.52
5070 7006 0.241213 GGAAAGAGTTTGCCGAAGCC 59.759 55.000 0.00 0.00 38.69 4.35
5071 7007 0.241213 GGGAAAGAGTTTGCCGAAGC 59.759 55.000 0.00 0.00 41.38 3.86
5077 7013 1.539157 CCTGGAGGGAAAGAGTTTGC 58.461 55.000 0.00 0.00 37.23 3.68
5078 7014 1.074566 AGCCTGGAGGGAAAGAGTTTG 59.925 52.381 0.00 0.00 37.23 2.93
5079 7015 1.352687 GAGCCTGGAGGGAAAGAGTTT 59.647 52.381 0.00 0.00 37.23 2.66
5080 7016 0.988063 GAGCCTGGAGGGAAAGAGTT 59.012 55.000 0.00 0.00 37.23 3.01
5081 7017 0.912006 GGAGCCTGGAGGGAAAGAGT 60.912 60.000 0.00 0.00 37.23 3.24
5082 7018 1.911471 GGAGCCTGGAGGGAAAGAG 59.089 63.158 0.00 0.00 37.23 2.85
5083 7019 1.990060 CGGAGCCTGGAGGGAAAGA 60.990 63.158 0.00 0.00 37.23 2.52
5084 7020 2.586792 CGGAGCCTGGAGGGAAAG 59.413 66.667 0.00 0.00 37.23 2.62
5097 7033 1.140852 TCCATGGACTAATTGGCGGAG 59.859 52.381 11.44 0.00 0.00 4.63
5098 7034 1.208706 TCCATGGACTAATTGGCGGA 58.791 50.000 11.44 0.00 0.00 5.54
5099 7035 2.276732 ATCCATGGACTAATTGGCGG 57.723 50.000 18.99 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.