Multiple sequence alignment - TraesCS2A01G502400

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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 TraesCS2A01G502400 chr2A 100.000 7914 0 0 1 7914 731163761 731155848 0.000000e+00 14615.0
1 TraesCS2A01G502400 chr2D 94.005 7173 253 65 772 7846 596917719 596910626 0.000000e+00 10700.0
2 TraesCS2A01G502400 chr2D 89.496 695 43 14 3 691 596918665 596917995 0.000000e+00 852.0
3 TraesCS2A01G502400 chr2B 95.615 3991 122 28 3294 7243 725963954 725959976 0.000000e+00 6351.0
4 TraesCS2A01G502400 chr2B 91.235 2179 109 40 921 3082 725966380 725964267 0.000000e+00 2891.0
5 TraesCS2A01G502400 chr2B 89.383 697 44 14 4 694 725967463 725966791 0.000000e+00 850.0
6 TraesCS2A01G502400 chr2B 88.558 437 23 12 7423 7846 725959863 725959441 9.170000e-139 505.0
7 TraesCS2A01G502400 chr2B 93.038 158 8 3 3081 3236 725964107 725963951 2.220000e-55 228.0
8 TraesCS2A01G502400 chr2B 94.643 56 3 0 7848 7903 725959408 725959353 3.930000e-13 87.9
9 TraesCS2A01G502400 chr6A 78.431 459 69 14 6442 6895 614862483 614862050 1.010000e-68 272.0
10 TraesCS2A01G502400 chr1A 83.065 248 36 4 2718 2962 450096399 450096155 3.720000e-53 220.0
11 TraesCS2A01G502400 chr1D 82.258 248 38 4 2718 2962 349794643 349794399 8.050000e-50 209.0


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 TraesCS2A01G502400 chr2A 731155848 731163761 7913 True 14615.000000 14615 100.000000 1 7914 1 chr2A.!!$R1 7913
1 TraesCS2A01G502400 chr2D 596910626 596918665 8039 True 5776.000000 10700 91.750500 3 7846 2 chr2D.!!$R1 7843
2 TraesCS2A01G502400 chr2B 725959353 725967463 8110 True 1818.816667 6351 92.078667 4 7903 6 chr2B.!!$R1 7899

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
310 327 0.250510 GGAATGGAATCTCCCTCCGC 60.251 60.000 0.00 0.00 35.03 5.54 F
862 1091 1.305887 TCCGGTTTCTCTCCTCCCC 60.306 63.158 0.00 0.00 0.00 4.81 F
1291 1532 0.761187 TCACCTGCTGTTCTTCTGCT 59.239 50.000 0.00 0.00 40.79 4.24 F
2648 2912 0.109226 GAAGGTGAGCGTCGCTACTT 60.109 55.000 21.77 22.66 39.88 2.24 F
2685 2949 0.813821 GGTGCCTGATTTCTTGCCTC 59.186 55.000 0.00 0.00 0.00 4.70 F
2763 3028 1.005805 CTGGGATTCATGTGGAACCCA 59.994 52.381 8.84 8.84 41.54 4.51 F
3856 4284 0.179004 TTTTGTCGGTCACCATGGCT 60.179 50.000 13.04 0.00 0.00 4.75 F
4615 5047 0.668535 GTCTGTTGCCCCTGTTTGAC 59.331 55.000 0.00 0.00 0.00 3.18 F
5911 6377 0.526211 CGGTGTCGAGTCAATCAGGA 59.474 55.000 0.00 0.00 39.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1391 0.102300 AGCGTCGCATACATACAGCA 59.898 50.000 21.09 0.0 0.00 4.41 R
1788 2051 0.449388 CCACTGCTGCTCGAAAATCC 59.551 55.000 0.00 0.0 0.00 3.01 R
2717 2982 0.739112 GAGGACTTTGCTCTCCTGCG 60.739 60.000 0.00 0.0 37.00 5.18 R
3565 3993 1.005097 TCAATCTCACCCTGCTTGCAT 59.995 47.619 0.00 0.0 0.00 3.96 R
3640 4068 1.102154 CTTGGTTGGTGCTGTCAACA 58.898 50.000 15.33 0.8 44.38 3.33 R
3865 4293 1.174712 CCTGCTGGGACAACTTGTGG 61.175 60.000 0.00 0.0 38.70 4.17 R
5717 6176 0.253327 CCAGAGCAAGGTAGGTTCCC 59.747 60.000 0.00 0.0 0.00 3.97 R
6172 6638 0.940126 CGATTCCCTTGATCCTTGCG 59.060 55.000 0.00 0.0 0.00 4.85 R
7767 8284 0.953960 GAAAGCGAGCGGGGAAAGAA 60.954 55.000 0.00 0.0 0.00 2.52 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
83 84 1.460273 GCACCAACCAACCAACCGAT 61.460 55.000 0.00 0.00 0.00 4.18
117 118 3.044986 CTCGACTGTTGCCAAAAACATG 58.955 45.455 0.00 0.00 39.25 3.21
118 119 1.522258 CGACTGTTGCCAAAAACATGC 59.478 47.619 0.00 0.00 39.25 4.06
119 120 1.866601 GACTGTTGCCAAAAACATGCC 59.133 47.619 0.00 0.00 39.25 4.40
120 121 1.209019 ACTGTTGCCAAAAACATGCCA 59.791 42.857 0.00 0.00 39.25 4.92
121 122 1.868498 CTGTTGCCAAAAACATGCCAG 59.132 47.619 0.00 0.00 39.25 4.85
122 123 1.228533 GTTGCCAAAAACATGCCAGG 58.771 50.000 0.00 0.00 0.00 4.45
123 124 0.835941 TTGCCAAAAACATGCCAGGT 59.164 45.000 0.00 0.00 0.00 4.00
124 125 0.835941 TGCCAAAAACATGCCAGGTT 59.164 45.000 0.00 0.00 0.00 3.50
125 126 1.211457 TGCCAAAAACATGCCAGGTTT 59.789 42.857 0.92 0.92 39.99 3.27
126 127 2.435805 TGCCAAAAACATGCCAGGTTTA 59.564 40.909 8.01 0.00 37.47 2.01
127 128 2.805671 GCCAAAAACATGCCAGGTTTAC 59.194 45.455 8.01 0.00 37.47 2.01
128 129 3.742640 GCCAAAAACATGCCAGGTTTACA 60.743 43.478 8.01 0.00 37.47 2.41
129 130 4.057432 CCAAAAACATGCCAGGTTTACAG 58.943 43.478 8.01 1.64 37.47 2.74
130 131 3.385193 AAAACATGCCAGGTTTACAGC 57.615 42.857 8.01 0.00 37.47 4.40
168 169 0.835971 GGCAACAAAATCCCACCCCT 60.836 55.000 0.00 0.00 0.00 4.79
170 171 1.266178 CAACAAAATCCCACCCCTCC 58.734 55.000 0.00 0.00 0.00 4.30
171 172 1.167033 AACAAAATCCCACCCCTCCT 58.833 50.000 0.00 0.00 0.00 3.69
172 173 2.042433 CAACAAAATCCCACCCCTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
173 174 1.639108 ACAAAATCCCACCCCTCCTAC 59.361 52.381 0.00 0.00 0.00 3.18
174 175 1.923148 CAAAATCCCACCCCTCCTACT 59.077 52.381 0.00 0.00 0.00 2.57
175 176 3.120108 CAAAATCCCACCCCTCCTACTA 58.880 50.000 0.00 0.00 0.00 1.82
176 177 2.797285 AATCCCACCCCTCCTACTAG 57.203 55.000 0.00 0.00 0.00 2.57
178 179 0.929734 TCCCACCCCTCCTACTAGCT 60.930 60.000 0.00 0.00 0.00 3.32
310 327 0.250510 GGAATGGAATCTCCCTCCGC 60.251 60.000 0.00 0.00 35.03 5.54
311 328 0.250510 GAATGGAATCTCCCTCCGCC 60.251 60.000 0.00 0.00 35.03 6.13
312 329 1.709994 AATGGAATCTCCCTCCGCCC 61.710 60.000 0.00 0.00 35.03 6.13
313 330 2.446802 GGAATCTCCCTCCGCCCT 60.447 66.667 0.00 0.00 0.00 5.19
314 331 2.512355 GGAATCTCCCTCCGCCCTC 61.512 68.421 0.00 0.00 0.00 4.30
315 332 2.446802 AATCTCCCTCCGCCCTCC 60.447 66.667 0.00 0.00 0.00 4.30
316 333 3.332393 AATCTCCCTCCGCCCTCCA 62.332 63.158 0.00 0.00 0.00 3.86
317 334 2.628187 AATCTCCCTCCGCCCTCCAT 62.628 60.000 0.00 0.00 0.00 3.41
318 335 3.237741 CTCCCTCCGCCCTCCATC 61.238 72.222 0.00 0.00 0.00 3.51
319 336 4.880426 TCCCTCCGCCCTCCATCC 62.880 72.222 0.00 0.00 0.00 3.51
322 339 4.888325 CTCCGCCCTCCATCCCCT 62.888 72.222 0.00 0.00 0.00 4.79
323 340 4.880426 TCCGCCCTCCATCCCCTC 62.880 72.222 0.00 0.00 0.00 4.30
413 446 3.723348 GACCCTTTGACGCCGCAC 61.723 66.667 0.00 0.00 0.00 5.34
555 588 4.213482 GTCAAATCTTCGGGATATTTCCGG 59.787 45.833 15.39 0.00 46.78 5.14
694 728 2.811317 GGCACGCGAACAGAGAGG 60.811 66.667 15.93 0.00 0.00 3.69
696 730 2.125912 CACGCGAACAGAGAGGGG 60.126 66.667 15.93 0.00 0.00 4.79
712 746 3.793888 GGGGGCGGGTTAGGTGAG 61.794 72.222 0.00 0.00 0.00 3.51
713 747 3.793888 GGGGCGGGTTAGGTGAGG 61.794 72.222 0.00 0.00 0.00 3.86
714 748 3.793888 GGGCGGGTTAGGTGAGGG 61.794 72.222 0.00 0.00 0.00 4.30
715 749 4.484872 GGCGGGTTAGGTGAGGGC 62.485 72.222 0.00 0.00 0.00 5.19
716 750 4.484872 GCGGGTTAGGTGAGGGCC 62.485 72.222 0.00 0.00 0.00 5.80
717 751 3.793888 CGGGTTAGGTGAGGGCCC 61.794 72.222 16.46 16.46 36.08 5.80
718 752 2.612746 GGGTTAGGTGAGGGCCCA 60.613 66.667 27.56 0.00 39.13 5.36
719 753 2.675371 GGTTAGGTGAGGGCCCAC 59.325 66.667 27.56 20.25 36.37 4.61
763 797 4.570663 CCGGTTCGGCTCGCCTAG 62.571 72.222 6.35 0.00 41.17 3.02
764 798 4.570663 CGGTTCGGCTCGCCTAGG 62.571 72.222 3.67 3.67 0.00 3.02
765 799 4.222847 GGTTCGGCTCGCCTAGGG 62.223 72.222 11.72 0.44 0.00 3.53
842 1071 3.551407 GGAGACCTCCCCCATCGC 61.551 72.222 4.72 0.00 43.94 4.58
860 1089 1.962321 GCCTCCGGTTTCTCTCCTCC 61.962 65.000 0.00 0.00 0.00 4.30
861 1090 1.331399 CCTCCGGTTTCTCTCCTCCC 61.331 65.000 0.00 0.00 0.00 4.30
862 1091 1.305887 TCCGGTTTCTCTCCTCCCC 60.306 63.158 0.00 0.00 0.00 4.81
863 1092 2.722201 CCGGTTTCTCTCCTCCCCG 61.722 68.421 0.00 0.00 35.32 5.73
926 1155 4.219999 GCGGAGGAGAGAGCAGCC 62.220 72.222 0.00 0.00 0.00 4.85
1112 1346 4.806339 CGCTTCCCCCTCCCCTCT 62.806 72.222 0.00 0.00 0.00 3.69
1137 1371 3.358076 CTTCCGACGCCCTGTCTCC 62.358 68.421 0.00 0.00 45.87 3.71
1157 1391 1.647545 CGCGGTGATGCTTGGTTCAT 61.648 55.000 0.00 0.00 0.00 2.57
1244 1485 1.079503 GGAGAATCGCACCAACTGTC 58.920 55.000 0.00 0.00 34.37 3.51
1289 1530 2.032549 CGTTTCACCTGCTGTTCTTCTG 60.033 50.000 0.00 0.00 0.00 3.02
1290 1531 1.597742 TTCACCTGCTGTTCTTCTGC 58.402 50.000 0.00 0.00 40.62 4.26
1291 1532 0.761187 TCACCTGCTGTTCTTCTGCT 59.239 50.000 0.00 0.00 40.79 4.24
1391 1636 9.726232 ATCGAAAGTTTAACTGGTTACTTTTTC 57.274 29.630 12.61 11.12 28.11 2.29
1397 1642 9.016438 AGTTTAACTGGTTACTTTTTCTGTGAA 57.984 29.630 0.00 0.00 0.00 3.18
1407 1652 9.120422 GTTACTTTTTCTGTGAAAACGAAAAGA 57.880 29.630 13.55 0.00 37.76 2.52
1468 1713 0.941463 CGTATCTCGCCATGTGAGCC 60.941 60.000 7.21 0.00 39.69 4.70
1541 1787 1.168714 GCAGACACCCCATGTTTCTC 58.831 55.000 0.00 0.00 43.56 2.87
1802 2065 1.106285 AATGGGGATTTTCGAGCAGC 58.894 50.000 0.00 0.00 0.00 5.25
1805 2068 0.678048 GGGGATTTTCGAGCAGCAGT 60.678 55.000 0.00 0.00 0.00 4.40
1806 2069 0.449388 GGGATTTTCGAGCAGCAGTG 59.551 55.000 0.00 0.00 0.00 3.66
1811 2074 0.679505 TTTCGAGCAGCAGTGGTAGT 59.320 50.000 0.00 0.00 33.41 2.73
1849 2112 1.489230 GGATGGGAGTACGGATTTGGT 59.511 52.381 0.00 0.00 0.00 3.67
1930 2193 4.025401 GCCAACCACCACGAAGCG 62.025 66.667 0.00 0.00 0.00 4.68
2169 2432 1.073548 GGGGAAAAGTACGCACCCA 59.926 57.895 17.34 0.00 42.03 4.51
2170 2433 0.537828 GGGGAAAAGTACGCACCCAA 60.538 55.000 17.34 0.00 42.03 4.12
2246 2509 2.438975 ATCAGACGGCCGTACGGA 60.439 61.111 37.62 27.69 38.39 4.69
2248 2511 1.793134 ATCAGACGGCCGTACGGATC 61.793 60.000 37.62 27.53 38.39 3.36
2249 2512 3.214845 AGACGGCCGTACGGATCC 61.215 66.667 37.62 27.00 38.39 3.36
2291 2554 2.441001 CTCCTTGGTTGATAGATGCCCT 59.559 50.000 0.00 0.00 0.00 5.19
2380 2643 1.068127 ACGACGTGGAAGCTACTGTTT 59.932 47.619 3.97 0.00 0.00 2.83
2424 2687 4.065088 TGTGTGATTTGTCTGTTCTAGCC 58.935 43.478 0.00 0.00 0.00 3.93
2503 2767 4.436242 TGGTTTGTTTCGCTTGTGTTTA 57.564 36.364 0.00 0.00 0.00 2.01
2557 2821 0.603439 TCGAGCAGCTGAAATGCACA 60.603 50.000 20.43 0.00 46.31 4.57
2648 2912 0.109226 GAAGGTGAGCGTCGCTACTT 60.109 55.000 21.77 22.66 39.88 2.24
2674 2938 0.961019 GATGCAAGTTTGGTGCCTGA 59.039 50.000 0.00 0.00 41.49 3.86
2685 2949 0.813821 GGTGCCTGATTTCTTGCCTC 59.186 55.000 0.00 0.00 0.00 4.70
2698 2963 4.465632 TCTTGCCTCGTCTTAATTGCTA 57.534 40.909 0.00 0.00 0.00 3.49
2700 2965 2.901249 TGCCTCGTCTTAATTGCTACC 58.099 47.619 0.00 0.00 0.00 3.18
2702 2967 3.055385 TGCCTCGTCTTAATTGCTACCTT 60.055 43.478 0.00 0.00 0.00 3.50
2703 2968 3.309954 GCCTCGTCTTAATTGCTACCTTG 59.690 47.826 0.00 0.00 0.00 3.61
2704 2969 4.504858 CCTCGTCTTAATTGCTACCTTGT 58.495 43.478 0.00 0.00 0.00 3.16
2705 2970 4.330074 CCTCGTCTTAATTGCTACCTTGTG 59.670 45.833 0.00 0.00 0.00 3.33
2716 2981 1.409427 CTACCTTGTGGGGTCTCGATC 59.591 57.143 0.00 0.00 40.48 3.69
2717 2982 1.265454 ACCTTGTGGGGTCTCGATCC 61.265 60.000 0.00 0.00 40.03 3.36
2763 3028 1.005805 CTGGGATTCATGTGGAACCCA 59.994 52.381 8.84 8.84 41.54 4.51
2859 3124 3.131046 GGCAGGATTTCGTTGGAATCATT 59.869 43.478 0.61 0.00 30.88 2.57
3001 3266 5.195001 TGTCCTGTTAGGTTGCAATTTTC 57.805 39.130 0.59 0.00 36.53 2.29
3060 3326 6.650807 TCTGCTTCCAATGTACTTTTCTAGTG 59.349 38.462 0.00 0.00 37.73 2.74
3088 3514 8.621532 TGCTTTCAACTGTGATATAGAAGTTT 57.378 30.769 0.00 0.00 32.48 2.66
3297 3725 6.017192 GGTGGAAACTTGCTGCATTTATTTTT 60.017 34.615 1.84 0.00 0.00 1.94
3306 3734 9.749490 CTTGCTGCATTTATTTTTATTGAGTTG 57.251 29.630 1.84 0.00 0.00 3.16
3565 3993 4.705110 TGAGGTCTTTTCTGGATCAACA 57.295 40.909 0.00 0.00 0.00 3.33
3715 4143 2.949451 ACTTCTGCATCGTCTCGATT 57.051 45.000 1.82 0.00 44.59 3.34
3727 4155 2.359900 GTCTCGATTGCAGTGGGAATT 58.640 47.619 0.00 0.00 34.96 2.17
3856 4284 0.179004 TTTTGTCGGTCACCATGGCT 60.179 50.000 13.04 0.00 0.00 4.75
3865 4293 2.024414 GTCACCATGGCTATTGGTTCC 58.976 52.381 13.04 0.00 45.19 3.62
4287 4715 3.248363 GTGCAGCGATGCTTCATTACATA 59.752 43.478 27.55 0.00 36.40 2.29
4330 4758 9.630098 ATTGCATTGTTCTTTAATGTGACTAAG 57.370 29.630 0.00 0.00 37.73 2.18
4368 4797 8.561738 TGAAACTTGAACAGATTATTACCCTC 57.438 34.615 0.00 0.00 0.00 4.30
4422 4851 5.174395 GTGCACTCTGTGATTGAGAAGTAT 58.826 41.667 10.32 0.00 35.23 2.12
4615 5047 0.668535 GTCTGTTGCCCCTGTTTGAC 59.331 55.000 0.00 0.00 0.00 3.18
5074 5508 2.415893 GCACATTGTTGGTATGACTGGC 60.416 50.000 0.00 0.00 0.00 4.85
5408 5843 9.099454 GTGGTAAGTACCTCAAAGATATTTCTG 57.901 37.037 8.91 0.00 46.58 3.02
5414 5849 3.633986 CCTCAAAGATATTTCTGCCCACC 59.366 47.826 0.00 0.00 30.72 4.61
5419 5854 3.279434 AGATATTTCTGCCCACCGAAAC 58.721 45.455 0.00 0.00 32.55 2.78
5484 5919 3.721035 CTTGGCTTTATGCTTATTGCCC 58.279 45.455 15.74 2.00 42.00 5.36
5552 5987 5.764686 TGCCATTCTCAATGATGGTATGTAC 59.235 40.000 3.63 0.00 41.46 2.90
5563 5998 6.494893 TGATGGTATGTACTCTTTTGTTGC 57.505 37.500 0.00 0.00 0.00 4.17
5717 6176 2.723746 GCCACTGGTGTTGTGCTG 59.276 61.111 0.00 0.00 34.38 4.41
5736 6195 3.863407 GGAACCTACCTTGCTCTGG 57.137 57.895 0.00 0.00 0.00 3.86
5757 6216 1.000163 TGACTGTCGTCTTCTTCTGGC 60.000 52.381 2.98 0.00 40.86 4.85
5759 6218 1.271102 ACTGTCGTCTTCTTCTGGCTC 59.729 52.381 0.00 0.00 0.00 4.70
5783 6242 3.134458 CCACAAGACAGACTTCTTCACC 58.866 50.000 0.00 0.00 36.61 4.02
5845 6304 4.027674 TGCATTAAAACTGCTGGTAGGA 57.972 40.909 1.55 0.00 40.34 2.94
5850 6309 7.177568 TGCATTAAAACTGCTGGTAGGAAAATA 59.822 33.333 1.55 0.00 40.34 1.40
5879 6345 6.420903 GTGGGTTCTCACTTAAATTTCTTTGC 59.579 38.462 0.00 0.00 34.98 3.68
5899 6365 1.721489 CGCAGAACAAATTCGGTGTCG 60.721 52.381 0.00 0.00 40.04 4.35
5900 6366 1.529438 GCAGAACAAATTCGGTGTCGA 59.471 47.619 0.00 0.00 44.44 4.20
5911 6377 0.526211 CGGTGTCGAGTCAATCAGGA 59.474 55.000 0.00 0.00 39.00 3.86
5915 6381 2.731976 GTGTCGAGTCAATCAGGAACAC 59.268 50.000 0.00 0.00 0.00 3.32
5919 6385 2.609491 CGAGTCAATCAGGAACACCGAA 60.609 50.000 0.00 0.00 0.00 4.30
5923 6389 5.556915 AGTCAATCAGGAACACCGAATTTA 58.443 37.500 0.00 0.00 0.00 1.40
5926 6392 5.414454 TCAATCAGGAACACCGAATTTAAGG 59.586 40.000 0.00 0.00 0.00 2.69
5927 6393 4.627284 TCAGGAACACCGAATTTAAGGA 57.373 40.909 3.08 0.00 0.00 3.36
5991 6457 4.327627 GCTCTTATCTTTGTGACTCGTTCC 59.672 45.833 0.00 0.00 0.00 3.62
6018 6484 1.896660 GTCCTTTGTTGAGCGCCCA 60.897 57.895 2.29 0.00 0.00 5.36
6045 6511 0.611714 TCTTGGTTACCGCCTTCCTC 59.388 55.000 0.00 0.00 0.00 3.71
6067 6533 1.527736 TCGCACAATTGGTACGTGAAC 59.472 47.619 10.83 0.00 37.53 3.18
6079 6545 5.358090 TGGTACGTGAACAACAGTTTATCA 58.642 37.500 0.00 0.00 0.00 2.15
6089 6555 7.913297 TGAACAACAGTTTATCAGCAAAGTAAC 59.087 33.333 0.00 0.00 0.00 2.50
6098 6564 9.463443 GTTTATCAGCAAAGTAACAAATTCAGT 57.537 29.630 0.00 0.00 0.00 3.41
6126 6592 4.080863 TCCAATCCTTAGCTGAACCTTCTC 60.081 45.833 0.00 0.00 0.00 2.87
6169 6635 2.014068 GCTGTCTATGCCAACTGGGAC 61.014 57.143 0.00 0.00 38.75 4.46
6172 6638 2.027192 TGTCTATGCCAACTGGGACTTC 60.027 50.000 0.00 0.00 38.75 3.01
6220 6686 0.749454 GGGCTGGTGTTATCTGGCTG 60.749 60.000 0.00 0.00 0.00 4.85
6247 6713 3.437049 GCATTGTGTTCTACTTCCCACTC 59.563 47.826 0.00 0.00 0.00 3.51
6321 6787 4.523190 AACCTCCTGCAGAACAAGGTACT 61.523 47.826 22.22 11.05 39.40 2.73
6340 6806 6.711645 AGGTACTAAGTCGAACCATATCTCTC 59.288 42.308 4.61 0.00 36.02 3.20
6356 6822 4.462508 TCTCTCTGTCAGCACCTTTATG 57.537 45.455 0.00 0.00 0.00 1.90
6383 6852 4.791880 AGGTACACATATGGGGTTTACCTT 59.208 41.667 16.44 5.24 45.13 3.50
6384 6853 4.885325 GGTACACATATGGGGTTTACCTTG 59.115 45.833 10.35 0.00 38.14 3.61
6386 6855 4.595986 ACACATATGGGGTTTACCTTGTC 58.404 43.478 10.35 0.00 40.03 3.18
6481 6950 1.037579 GGGAAGCACAATGGGCTACC 61.038 60.000 11.67 13.11 41.66 3.18
6514 6983 2.703798 CCATGGCCTTCAAGCACCG 61.704 63.158 3.32 0.00 0.00 4.94
6651 7120 8.049117 ACTTCCAAATTGCTAATAGATCAGACA 58.951 33.333 0.00 0.00 0.00 3.41
6655 7124 7.930325 CCAAATTGCTAATAGATCAGACAGAGA 59.070 37.037 0.00 0.00 0.00 3.10
6672 7141 2.685897 AGAGACAGGCTAGTCGTTGATC 59.314 50.000 10.14 0.00 43.24 2.92
6690 7161 0.618458 TCGCTAATGCCCTTTCCTGT 59.382 50.000 0.00 0.00 35.36 4.00
6698 7169 5.603170 AATGCCCTTTCCTGTTGATTATG 57.397 39.130 0.00 0.00 0.00 1.90
6808 7279 3.399330 ACTACACCGTGTGAGGAAATTG 58.601 45.455 14.66 0.00 36.96 2.32
6838 7309 2.293122 ACCAACAAACATGACATCCGTG 59.707 45.455 0.00 0.00 37.78 4.94
7115 7587 4.339872 AATCACTGCAAATTTTCTGCCA 57.660 36.364 0.00 0.00 39.13 4.92
7136 7608 2.092267 ACATGCTTGCTATCCCATCACA 60.092 45.455 0.00 0.00 0.00 3.58
7208 7680 3.953612 TCTGCAATGGAGTTTCAAAGTGT 59.046 39.130 0.85 0.00 0.00 3.55
7267 7739 1.561076 TGCTATCATTGCCAGTGGACT 59.439 47.619 15.20 0.00 0.00 3.85
7293 7765 2.228115 GTGCAGCACAATTTGGCAC 58.772 52.632 21.22 11.11 46.53 5.01
7294 7766 1.069427 TGCAGCACAATTTGGCACC 59.931 52.632 10.96 3.97 0.00 5.01
7296 7768 0.532417 GCAGCACAATTTGGCACCAA 60.532 50.000 0.00 0.00 0.00 3.67
7318 7793 7.367159 CAACTTACGTTGGGATGTTTATGTA 57.633 36.000 4.22 0.00 45.28 2.29
7337 7812 4.968259 TGTAGTTAGCCACACATTTGAGT 58.032 39.130 0.00 0.00 0.00 3.41
7338 7813 4.754618 TGTAGTTAGCCACACATTTGAGTG 59.245 41.667 1.68 1.68 44.93 3.51
7342 7817 6.237901 AGTTAGCCACACATTTGAGTGAATA 58.762 36.000 9.32 0.56 42.05 1.75
7347 7822 5.391310 GCCACACATTTGAGTGAATAGTGAG 60.391 44.000 9.32 0.00 42.05 3.51
7348 7823 5.391310 CCACACATTTGAGTGAATAGTGAGC 60.391 44.000 9.32 0.00 42.05 4.26
7379 7883 4.532916 TGTGTAAAGGTAGCTGGTTATGGA 59.467 41.667 0.00 0.00 0.00 3.41
7380 7884 4.874396 GTGTAAAGGTAGCTGGTTATGGAC 59.126 45.833 0.00 0.00 0.00 4.02
7382 7886 3.629142 AAGGTAGCTGGTTATGGACAC 57.371 47.619 0.00 0.00 0.00 3.67
7406 7910 5.288804 CACGTTGGTTGAAGAAATCCAAAT 58.711 37.500 0.00 0.00 40.82 2.32
7427 7931 2.938451 TGAATTCGGCAGCAGTATTCTG 59.062 45.455 20.15 0.00 43.87 3.02
7508 8012 4.178540 CGGAAAGCGAGGTGTAGATAAAA 58.821 43.478 0.00 0.00 0.00 1.52
7539 8044 2.202756 GGAGAGTTAGCCGCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
7552 8057 2.202797 CCGTGCCGTCATCCTCAG 60.203 66.667 0.00 0.00 0.00 3.35
7595 8100 1.752501 CGGCTATTCTTCCACGCACG 61.753 60.000 0.00 0.00 0.00 5.34
7596 8101 0.459585 GGCTATTCTTCCACGCACGA 60.460 55.000 0.00 0.00 0.00 4.35
7597 8102 1.355971 GCTATTCTTCCACGCACGAA 58.644 50.000 0.00 0.00 0.00 3.85
7598 8103 1.324736 GCTATTCTTCCACGCACGAAG 59.675 52.381 0.00 1.36 38.47 3.79
7608 8113 0.667792 ACGCACGAAGAGAAAGCTCC 60.668 55.000 0.00 0.00 42.30 4.70
7699 8216 2.357034 CGACCCACCACCACTTCG 60.357 66.667 0.00 0.00 0.00 3.79
7703 8220 2.260869 CCCACCACCACTTCGCAAG 61.261 63.158 0.00 0.00 0.00 4.01
7736 8253 1.152756 AACCTGTTCACTGCACCCC 60.153 57.895 0.00 0.00 0.00 4.95
7759 8276 4.114997 CGCCGTTGCATTCCACCC 62.115 66.667 0.00 0.00 37.32 4.61
7767 8284 1.698506 TGCATTCCACCCTTTCGTTT 58.301 45.000 0.00 0.00 0.00 3.60
7846 8363 1.935873 GTCTATCAAAGAGCATGCGCA 59.064 47.619 23.73 14.96 42.27 6.09
7897 8445 2.490217 CACCGAGCCGTAGTCCTG 59.510 66.667 0.00 0.00 0.00 3.86
7903 8451 0.971447 GAGCCGTAGTCCTGGGTCTT 60.971 60.000 3.36 0.00 0.00 3.01
7904 8452 0.971447 AGCCGTAGTCCTGGGTCTTC 60.971 60.000 0.00 0.00 0.00 2.87
7905 8453 1.255667 GCCGTAGTCCTGGGTCTTCA 61.256 60.000 0.00 0.00 0.00 3.02
7906 8454 0.818296 CCGTAGTCCTGGGTCTTCAG 59.182 60.000 0.00 0.00 34.70 3.02
7907 8455 1.616187 CCGTAGTCCTGGGTCTTCAGA 60.616 57.143 0.00 0.00 36.93 3.27
7908 8456 1.473278 CGTAGTCCTGGGTCTTCAGAC 59.527 57.143 0.00 0.00 44.04 3.51
7909 8457 2.810164 GTAGTCCTGGGTCTTCAGACT 58.190 52.381 6.91 0.00 44.20 3.24
7910 8458 2.407340 AGTCCTGGGTCTTCAGACTT 57.593 50.000 6.91 0.00 44.20 3.01
7911 8459 2.695585 AGTCCTGGGTCTTCAGACTTT 58.304 47.619 6.91 0.00 44.20 2.66
7912 8460 2.635427 AGTCCTGGGTCTTCAGACTTTC 59.365 50.000 6.91 0.00 44.20 2.62
7913 8461 2.635427 GTCCTGGGTCTTCAGACTTTCT 59.365 50.000 6.91 0.00 44.20 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 2.671619 TGGCGCTGTAAACCTGGC 60.672 61.111 7.64 0.00 0.00 4.85
118 119 2.040544 CCTGGCGCTGTAAACCTGG 61.041 63.158 7.64 0.00 36.40 4.45
119 120 0.889186 AACCTGGCGCTGTAAACCTG 60.889 55.000 7.64 0.00 0.00 4.00
120 121 0.179001 AAACCTGGCGCTGTAAACCT 60.179 50.000 7.64 0.00 0.00 3.50
121 122 1.198408 GTAAACCTGGCGCTGTAAACC 59.802 52.381 7.64 0.00 0.00 3.27
122 123 1.874872 TGTAAACCTGGCGCTGTAAAC 59.125 47.619 7.64 5.35 0.00 2.01
123 124 2.147958 CTGTAAACCTGGCGCTGTAAA 58.852 47.619 7.64 0.00 0.00 2.01
124 125 1.803334 CTGTAAACCTGGCGCTGTAA 58.197 50.000 7.64 0.00 0.00 2.41
125 126 0.672401 GCTGTAAACCTGGCGCTGTA 60.672 55.000 7.64 0.00 0.00 2.74
126 127 1.966451 GCTGTAAACCTGGCGCTGT 60.966 57.895 7.64 0.00 0.00 4.40
127 128 2.870372 GCTGTAAACCTGGCGCTG 59.130 61.111 7.64 0.00 0.00 5.18
128 129 2.742372 CGCTGTAAACCTGGCGCT 60.742 61.111 7.64 0.00 41.08 5.92
310 327 3.164269 CACGGAGGGGATGGAGGG 61.164 72.222 0.00 0.00 0.00 4.30
311 328 2.041922 TCACGGAGGGGATGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
312 329 2.435693 GGTCACGGAGGGGATGGAG 61.436 68.421 0.00 0.00 0.00 3.86
313 330 2.365105 GGTCACGGAGGGGATGGA 60.365 66.667 0.00 0.00 0.00 3.41
314 331 3.480133 GGGTCACGGAGGGGATGG 61.480 72.222 0.00 0.00 0.00 3.51
315 332 3.849951 CGGGTCACGGAGGGGATG 61.850 72.222 0.00 0.00 39.42 3.51
316 333 4.070265 TCGGGTCACGGAGGGGAT 62.070 66.667 0.00 0.00 44.45 3.85
317 334 4.753662 CTCGGGTCACGGAGGGGA 62.754 72.222 0.00 0.00 44.45 4.81
645 678 4.862823 CGTCCCTCCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
646 679 4.862823 CCGTCCCTCCCTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
696 730 3.793888 CCTCACCTAACCCGCCCC 61.794 72.222 0.00 0.00 0.00 5.80
698 732 4.484872 GCCCTCACCTAACCCGCC 62.485 72.222 0.00 0.00 0.00 6.13
699 733 4.484872 GGCCCTCACCTAACCCGC 62.485 72.222 0.00 0.00 0.00 6.13
700 734 3.793888 GGGCCCTCACCTAACCCG 61.794 72.222 17.04 0.00 0.00 5.28
701 735 2.612746 TGGGCCCTCACCTAACCC 60.613 66.667 25.70 0.00 41.24 4.11
702 736 2.675371 GTGGGCCCTCACCTAACC 59.325 66.667 25.70 0.00 0.00 2.85
747 781 4.570663 CCTAGGCGAGCCGAACCG 62.571 72.222 8.63 0.00 41.95 4.44
748 782 4.222847 CCCTAGGCGAGCCGAACC 62.223 72.222 2.05 0.00 41.95 3.62
749 783 4.893601 GCCCTAGGCGAGCCGAAC 62.894 72.222 2.05 0.00 39.62 3.95
759 793 3.706373 ACACCGTGCAGCCCTAGG 61.706 66.667 0.06 0.06 0.00 3.02
760 794 2.434884 CACACCGTGCAGCCCTAG 60.435 66.667 0.00 0.00 0.00 3.02
761 795 4.015406 CCACACCGTGCAGCCCTA 62.015 66.667 0.00 0.00 31.34 3.53
790 1019 1.564348 CTGCTTTATACCCACCCACCT 59.436 52.381 0.00 0.00 0.00 4.00
863 1092 4.660938 GAGTGGTGGTGGGTGGGC 62.661 72.222 0.00 0.00 0.00 5.36
888 1117 1.001760 CGGAGAAGGAAGGGAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
889 1118 2.066999 CCGGAGAAGGAAGGGAGGG 61.067 68.421 0.00 0.00 0.00 4.30
890 1119 1.001760 TCCGGAGAAGGAAGGGAGG 59.998 63.158 0.00 0.00 37.36 4.30
944 1178 4.514577 CCCGGCTCTACCACGCAG 62.515 72.222 0.00 0.00 39.03 5.18
1105 1339 0.548989 CGGAAGAGAGAGAGAGGGGA 59.451 60.000 0.00 0.00 0.00 4.81
1106 1340 0.548989 TCGGAAGAGAGAGAGAGGGG 59.451 60.000 0.00 0.00 34.84 4.79
1107 1341 1.675552 GTCGGAAGAGAGAGAGAGGG 58.324 60.000 0.00 0.00 43.49 4.30
1108 1342 1.295792 CGTCGGAAGAGAGAGAGAGG 58.704 60.000 0.00 0.00 43.49 3.69
1109 1343 0.655733 GCGTCGGAAGAGAGAGAGAG 59.344 60.000 0.00 0.00 43.49 3.20
1110 1344 0.745128 GGCGTCGGAAGAGAGAGAGA 60.745 60.000 0.00 0.00 43.49 3.10
1111 1345 1.720694 GGGCGTCGGAAGAGAGAGAG 61.721 65.000 0.00 0.00 43.49 3.20
1112 1346 1.749638 GGGCGTCGGAAGAGAGAGA 60.750 63.158 0.00 0.00 43.49 3.10
1137 1371 3.039202 GAACCAAGCATCACCGCGG 62.039 63.158 26.86 26.86 36.85 6.46
1157 1391 0.102300 AGCGTCGCATACATACAGCA 59.898 50.000 21.09 0.00 0.00 4.41
1237 1478 6.802348 CGGATTAATCTATCCTACGACAGTTG 59.198 42.308 14.95 0.00 41.65 3.16
1244 1485 4.673441 CCAGCGGATTAATCTATCCTACG 58.327 47.826 14.95 9.09 41.65 3.51
1289 1530 8.360390 CCAGTAATAATAATTCCCCAAAAGAGC 58.640 37.037 0.00 0.00 0.00 4.09
1290 1531 8.360390 GCCAGTAATAATAATTCCCCAAAAGAG 58.640 37.037 0.00 0.00 0.00 2.85
1291 1532 7.013846 CGCCAGTAATAATAATTCCCCAAAAGA 59.986 37.037 0.00 0.00 0.00 2.52
1331 1573 1.653151 AAAAGCTACGCGGATTCCTC 58.347 50.000 12.47 0.00 0.00 3.71
1334 1576 6.864560 AAAAATTAAAAGCTACGCGGATTC 57.135 33.333 12.47 0.00 0.00 2.52
1368 1613 9.850628 ACAGAAAAAGTAACCAGTTAAACTTTC 57.149 29.630 10.37 9.83 0.00 2.62
1391 1636 9.296400 TCCTTTAATTTCTTTTCGTTTTCACAG 57.704 29.630 0.00 0.00 0.00 3.66
1468 1713 0.743701 ATTGAAGAGCCGCTGAGCAG 60.744 55.000 4.88 0.00 34.23 4.24
1541 1787 4.547859 CGGGAGCAAATCAGAGGG 57.452 61.111 0.00 0.00 0.00 4.30
1681 1944 1.588139 GCTCGTATCCCGTTCCACG 60.588 63.158 0.00 0.00 42.11 4.94
1788 2051 0.449388 CCACTGCTGCTCGAAAATCC 59.551 55.000 0.00 0.00 0.00 3.01
1805 2068 9.103582 TCCCACTAATTCTACTAAAAACTACCA 57.896 33.333 0.00 0.00 0.00 3.25
1811 2074 8.165267 TCCCATCCCACTAATTCTACTAAAAA 57.835 34.615 0.00 0.00 0.00 1.94
1849 2112 8.774586 GTGCTTAACTATCTTTTGACTTCAAGA 58.225 33.333 0.00 0.00 37.15 3.02
2067 2330 2.590092 GCCAAGATGCGTACCCCT 59.410 61.111 0.00 0.00 0.00 4.79
2115 2378 2.874780 GCTCGTACGCACTCACCG 60.875 66.667 11.24 0.00 0.00 4.94
2150 2413 2.036571 GGGTGCGTACTTTTCCCCG 61.037 63.158 3.01 0.00 32.66 5.73
2169 2432 4.729856 GACCGTACGCGCCTGGTT 62.730 66.667 16.46 2.79 34.12 3.67
2276 2539 2.439507 TCCAAGAGGGCATCTATCAACC 59.560 50.000 0.44 0.00 37.23 3.77
2405 2668 3.326747 ACGGCTAGAACAGACAAATCAC 58.673 45.455 0.00 0.00 29.64 3.06
2424 2687 2.126307 CCCACTCAGTCAGCGACG 60.126 66.667 0.00 0.00 37.67 5.12
2503 2767 3.205056 TGGGGATGTTCTCCTGCAAATAT 59.795 43.478 0.00 0.00 44.28 1.28
2648 2912 3.737663 GCACCAAACTTGCATCAGAAACA 60.738 43.478 0.00 0.00 39.93 2.83
2674 2938 4.702131 AGCAATTAAGACGAGGCAAGAAAT 59.298 37.500 0.00 0.00 0.00 2.17
2685 2949 3.374058 CCCACAAGGTAGCAATTAAGACG 59.626 47.826 0.00 0.00 0.00 4.18
2698 2963 1.265454 GGATCGAGACCCCACAAGGT 61.265 60.000 0.00 0.00 45.12 3.50
2700 2965 1.141881 CGGATCGAGACCCCACAAG 59.858 63.158 5.96 0.00 0.00 3.16
2702 2967 3.458163 GCGGATCGAGACCCCACA 61.458 66.667 5.96 0.00 0.00 4.17
2703 2968 3.432051 CTGCGGATCGAGACCCCAC 62.432 68.421 5.96 0.00 0.00 4.61
2704 2969 3.147595 CTGCGGATCGAGACCCCA 61.148 66.667 5.96 2.98 0.00 4.96
2705 2970 3.917760 CCTGCGGATCGAGACCCC 61.918 72.222 0.00 0.00 0.00 4.95
2716 2981 1.743252 GGACTTTGCTCTCCTGCGG 60.743 63.158 0.00 0.00 35.36 5.69
2717 2982 0.739112 GAGGACTTTGCTCTCCTGCG 60.739 60.000 0.00 0.00 37.00 5.18
2859 3124 2.303022 GGAGTTGATGACCAGGAGAACA 59.697 50.000 0.00 0.00 0.00 3.18
3047 3313 4.755123 TGAAAGCAGGCACTAGAAAAGTAC 59.245 41.667 0.00 0.00 35.76 2.73
3060 3326 5.118990 TCTATATCACAGTTGAAAGCAGGC 58.881 41.667 0.00 0.00 34.61 4.85
3297 3725 6.091441 GGCAAACAAACAAACACAACTCAATA 59.909 34.615 0.00 0.00 0.00 1.90
3306 3734 3.938334 AGAATGGGCAAACAAACAAACAC 59.062 39.130 0.00 0.00 0.00 3.32
3565 3993 1.005097 TCAATCTCACCCTGCTTGCAT 59.995 47.619 0.00 0.00 0.00 3.96
3640 4068 1.102154 CTTGGTTGGTGCTGTCAACA 58.898 50.000 15.33 0.80 44.38 3.33
3688 4116 2.002586 ACGATGCAGAAGTTTCCGATG 58.997 47.619 0.00 0.00 0.00 3.84
3715 4143 2.821378 CTCAATGACAATTCCCACTGCA 59.179 45.455 0.00 0.00 0.00 4.41
3727 4155 5.014808 ACATGACGATGATCTCAATGACA 57.985 39.130 0.00 0.00 33.36 3.58
3865 4293 1.174712 CCTGCTGGGACAACTTGTGG 61.175 60.000 0.00 0.00 38.70 4.17
4081 4509 2.303600 ACCAACCATGCAAGCATCAATT 59.696 40.909 4.24 0.00 33.90 2.32
4299 4727 9.755804 TCACATTAAAGAACAATGCAATTAACA 57.244 25.926 0.00 0.00 36.96 2.41
4307 4735 7.816640 TCCTTAGTCACATTAAAGAACAATGC 58.183 34.615 0.00 0.00 36.96 3.56
4321 4749 5.778241 TCATACCAAGTCTTCCTTAGTCACA 59.222 40.000 0.00 0.00 0.00 3.58
4330 4758 6.262273 TGTTCAAGTTTCATACCAAGTCTTCC 59.738 38.462 0.00 0.00 0.00 3.46
4455 4884 9.187996 AGTATTAGAAGTTAAGGTACCTGTCTC 57.812 37.037 17.14 8.28 0.00 3.36
4957 5390 7.936496 TCATTGCATAACCAAACAGATAAGA 57.064 32.000 0.00 0.00 0.00 2.10
4986 5419 7.721402 TGCATAACACAAACCAAGTTAAGAAT 58.279 30.769 0.00 0.00 32.18 2.40
4989 5423 6.734137 TCTGCATAACACAAACCAAGTTAAG 58.266 36.000 0.00 0.00 32.18 1.85
4995 5429 2.954989 TGCTCTGCATAACACAAACCAA 59.045 40.909 0.00 0.00 31.71 3.67
5074 5508 1.600957 GGAGCATCATTGACACCATCG 59.399 52.381 0.00 0.00 36.25 3.84
5230 5664 3.444034 CCGTGTAGTTCTTCATCCTCTGA 59.556 47.826 0.00 0.00 0.00 3.27
5408 5843 3.249973 GAAGTGCGTTTCGGTGGGC 62.250 63.158 0.00 0.00 0.00 5.36
5414 5849 4.092821 TGGAGAAATATGAAGTGCGTTTCG 59.907 41.667 0.00 0.00 34.79 3.46
5484 5919 5.888105 AGCGAAATCAAATTTCCAGATCAG 58.112 37.500 6.79 0.00 44.40 2.90
5552 5987 4.142381 GGCTACTAATGGGCAACAAAAGAG 60.142 45.833 0.00 0.00 39.74 2.85
5581 6016 5.151297 TGTGAGAAGTTATGCTGACATGA 57.849 39.130 0.00 0.00 37.04 3.07
5582 6017 6.432607 AATGTGAGAAGTTATGCTGACATG 57.567 37.500 0.00 0.00 37.04 3.21
5717 6176 0.253327 CCAGAGCAAGGTAGGTTCCC 59.747 60.000 0.00 0.00 0.00 3.97
5757 6216 4.533919 AGAAGTCTGTCTTGTGGATGAG 57.466 45.455 0.00 0.00 36.40 2.90
5759 6218 4.450419 GTGAAGAAGTCTGTCTTGTGGATG 59.550 45.833 0.00 0.00 37.98 3.51
5815 6274 8.917088 ACCAGCAGTTTTAATGCAAAGATATAT 58.083 29.630 0.00 0.00 46.31 0.86
5817 6276 7.174107 ACCAGCAGTTTTAATGCAAAGATAT 57.826 32.000 0.00 0.00 46.31 1.63
5829 6288 8.107095 ACTGATATTTTCCTACCAGCAGTTTTA 58.893 33.333 0.00 0.00 30.66 1.52
5830 6289 6.948309 ACTGATATTTTCCTACCAGCAGTTTT 59.052 34.615 0.00 0.00 30.66 2.43
5836 6295 4.137543 CCCACTGATATTTTCCTACCAGC 58.862 47.826 0.00 0.00 0.00 4.85
5845 6304 8.934023 TTTAAGTGAGAACCCACTGATATTTT 57.066 30.769 0.00 0.00 45.82 1.82
5850 6309 7.234355 AGAAATTTAAGTGAGAACCCACTGAT 58.766 34.615 0.00 0.00 45.82 2.90
5879 6345 1.721489 CGACACCGAATTTGTTCTGCG 60.721 52.381 0.00 0.00 38.22 5.18
5899 6365 2.743636 TCGGTGTTCCTGATTGACTC 57.256 50.000 0.00 0.00 0.00 3.36
5900 6366 3.703001 ATTCGGTGTTCCTGATTGACT 57.297 42.857 0.00 0.00 0.00 3.41
5911 6377 5.643777 CAGACATCTCCTTAAATTCGGTGTT 59.356 40.000 0.00 0.00 0.00 3.32
5915 6381 4.034510 GTGCAGACATCTCCTTAAATTCGG 59.965 45.833 0.00 0.00 0.00 4.30
5919 6385 5.171339 ACAGTGCAGACATCTCCTTAAAT 57.829 39.130 0.00 0.00 0.00 1.40
5923 6389 2.234908 GGTACAGTGCAGACATCTCCTT 59.765 50.000 0.00 0.00 0.00 3.36
5926 6392 2.159170 GGAGGTACAGTGCAGACATCTC 60.159 54.545 0.00 0.00 0.00 2.75
5927 6393 1.827969 GGAGGTACAGTGCAGACATCT 59.172 52.381 0.00 0.00 0.00 2.90
5991 6457 1.156736 CAACAAAGGACCAGCTACGG 58.843 55.000 0.00 0.00 0.00 4.02
6018 6484 1.271217 GCGGTAACCAAGAGGAAACCT 60.271 52.381 0.00 0.00 39.53 3.50
6067 6533 8.627487 TTTGTTACTTTGCTGATAAACTGTTG 57.373 30.769 0.00 0.00 0.00 3.33
6079 6545 8.082242 GGATTGTACTGAATTTGTTACTTTGCT 58.918 33.333 0.00 0.00 0.00 3.91
6089 6555 7.917505 GCTAAGGATTGGATTGTACTGAATTTG 59.082 37.037 0.00 0.00 0.00 2.32
6098 6564 5.191722 AGGTTCAGCTAAGGATTGGATTGTA 59.808 40.000 0.00 0.00 0.00 2.41
6169 6635 2.113860 TTCCCTTGATCCTTGCGAAG 57.886 50.000 0.00 0.00 0.00 3.79
6172 6638 0.940126 CGATTCCCTTGATCCTTGCG 59.060 55.000 0.00 0.00 0.00 4.85
6220 6686 4.083271 GGGAAGTAGAACACAATGCTGAAC 60.083 45.833 0.00 0.00 0.00 3.18
6247 6713 5.082059 CGGATGAAGAACTTGAAAATGTCG 58.918 41.667 0.00 0.00 0.00 4.35
6321 6787 6.120220 TGACAGAGAGATATGGTTCGACTTA 58.880 40.000 0.00 0.00 0.00 2.24
6340 6806 5.003804 ACCTAAACATAAAGGTGCTGACAG 58.996 41.667 0.00 0.00 44.53 3.51
6356 6822 6.543465 GGTAAACCCCATATGTGTACCTAAAC 59.457 42.308 1.24 0.00 41.50 2.01
6383 6852 1.278985 AGGGTCATCATTTGCTCGACA 59.721 47.619 0.00 0.00 0.00 4.35
6384 6853 1.936547 GAGGGTCATCATTTGCTCGAC 59.063 52.381 0.00 0.00 0.00 4.20
6386 6855 1.938577 CAGAGGGTCATCATTTGCTCG 59.061 52.381 0.00 0.00 0.00 5.03
6481 6950 1.073964 CATGGAGTGTTCTCTGTGCG 58.926 55.000 0.00 0.00 40.29 5.34
6651 7120 2.201921 TCAACGACTAGCCTGTCTCT 57.798 50.000 0.00 0.00 35.00 3.10
6655 7124 0.179134 GCGATCAACGACTAGCCTGT 60.179 55.000 0.00 0.00 45.77 4.00
6672 7141 1.133025 CAACAGGAAAGGGCATTAGCG 59.867 52.381 0.00 0.00 43.41 4.26
6690 7161 3.010027 TCCCTCAACCTGCACATAATCAA 59.990 43.478 0.00 0.00 0.00 2.57
6698 7169 1.376553 GAGCTCCCTCAACCTGCAC 60.377 63.158 0.87 0.00 38.03 4.57
6808 7279 4.744631 GTCATGTTTGTTGGTTCAATGTCC 59.255 41.667 0.00 0.00 0.00 4.02
6838 7309 4.133078 CTCCATTCCAATCTAGCTCCAAC 58.867 47.826 0.00 0.00 0.00 3.77
7115 7587 2.092267 TGTGATGGGATAGCAAGCATGT 60.092 45.455 0.00 0.00 0.00 3.21
7136 7608 7.610305 ACGAGAATTGTCTTTGTATAAACCCAT 59.390 33.333 0.66 0.00 32.80 4.00
7180 7652 5.850557 TGAAACTCCATTGCAGAAAAAGA 57.149 34.783 0.00 0.00 0.00 2.52
7182 7654 6.313411 CACTTTGAAACTCCATTGCAGAAAAA 59.687 34.615 0.00 0.00 0.00 1.94
7267 7739 2.702040 ATTGTGCTGCACAGGAGCCA 62.702 55.000 31.27 18.61 45.39 4.75
7307 7779 6.978343 TGTGTGGCTAACTACATAAACATC 57.022 37.500 0.00 0.00 0.00 3.06
7318 7793 4.085357 TCACTCAAATGTGTGGCTAACT 57.915 40.909 13.74 0.00 39.30 2.24
7337 7812 5.234752 ACACAATTACGTGCTCACTATTCA 58.765 37.500 0.00 0.00 40.73 2.57
7338 7813 5.779806 ACACAATTACGTGCTCACTATTC 57.220 39.130 0.00 0.00 40.73 1.75
7342 7817 4.451096 CCTTTACACAATTACGTGCTCACT 59.549 41.667 0.00 0.00 40.73 3.41
7347 7822 4.390909 AGCTACCTTTACACAATTACGTGC 59.609 41.667 0.00 0.00 40.73 5.34
7348 7823 5.163893 CCAGCTACCTTTACACAATTACGTG 60.164 44.000 0.00 0.00 42.81 4.49
7382 7886 2.621055 TGGATTTCTTCAACCAACGTGG 59.379 45.455 0.00 0.00 45.02 4.94
7406 7910 2.938451 CAGAATACTGCTGCCGAATTCA 59.062 45.455 6.22 0.00 37.33 2.57
7427 7931 1.136984 CTGTCCTCGTCTGGCGTAC 59.863 63.158 0.09 0.00 42.13 3.67
7488 7992 7.073342 ACAATTTTATCTACACCTCGCTTTC 57.927 36.000 0.00 0.00 0.00 2.62
7497 8001 8.452989 CTTGCAAGGAACAATTTTATCTACAC 57.547 34.615 19.14 0.00 0.00 2.90
7539 8044 1.064654 GCATTTTCTGAGGATGACGGC 59.935 52.381 6.54 0.00 0.00 5.68
7578 8083 1.324736 CTTCGTGCGTGGAAGAATAGC 59.675 52.381 5.55 0.00 42.74 2.97
7597 8102 1.554617 GCAGGAAGAGGAGCTTTCTCT 59.445 52.381 12.90 12.90 40.62 3.10
7598 8103 1.406751 GGCAGGAAGAGGAGCTTTCTC 60.407 57.143 9.26 9.26 40.62 2.87
7608 8113 4.168291 GGCGGAGGGCAGGAAGAG 62.168 72.222 0.00 0.00 46.16 2.85
7658 8175 1.400846 TCGTCCTCGGAAAGATTCTCG 59.599 52.381 0.00 0.00 37.69 4.04
7699 8216 1.693627 TCGACCCTATCTCTCCTTGC 58.306 55.000 0.00 0.00 0.00 4.01
7703 8220 1.957877 CAGGTTCGACCCTATCTCTCC 59.042 57.143 0.00 0.00 39.75 3.71
7759 8276 1.607148 AGCGGGGAAAGAAAACGAAAG 59.393 47.619 0.00 0.00 0.00 2.62
7767 8284 0.953960 GAAAGCGAGCGGGGAAAGAA 60.954 55.000 0.00 0.00 0.00 2.52
7878 8426 2.753043 GGACTACGGCTCGGTGGA 60.753 66.667 0.00 0.00 0.00 4.02
7881 8429 2.754658 CCAGGACTACGGCTCGGT 60.755 66.667 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.