Multiple sequence alignment - TraesCS1B01G053300

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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 TraesCS1B01G053300 chr1B 100.000 3809 0 0 1 3809 33970046 33973854 0.000000e+00 7035.0
1 TraesCS1B01G053300 chr1B 82.319 345 45 9 665 995 33925400 33925742 6.230000e-73 285.0
2 TraesCS1B01G053300 chr5B 97.150 2842 56 5 993 3809 572962018 572964859 0.000000e+00 4776.0
3 TraesCS1B01G053300 chr5B 96.753 154 5 0 1 154 437137143 437136990 1.360000e-64 257.0
4 TraesCS1B01G053300 chr5B 95.541 157 7 0 1 157 502345342 502345498 6.320000e-63 252.0
5 TraesCS1B01G053300 chr1D 89.235 353 24 9 151 502 20180162 20179823 2.720000e-116 429.0
6 TraesCS1B01G053300 chr1D 82.874 508 48 16 515 995 20179774 20179279 1.640000e-113 420.0
7 TraesCS1B01G053300 chr4B 98.684 152 2 0 1 152 585203872 585203721 1.740000e-68 270.0
8 TraesCS1B01G053300 chr4B 96.178 157 6 0 1 157 393769940 393769784 1.360000e-64 257.0
9 TraesCS1B01G053300 chr3B 97.368 152 3 1 1 152 561179716 561179866 1.360000e-64 257.0
10 TraesCS1B01G053300 chr3B 95.541 157 7 0 1 157 403691646 403691802 6.320000e-63 252.0
11 TraesCS1B01G053300 chr3B 94.904 157 8 0 1 157 403576065 403575909 2.940000e-61 246.0
12 TraesCS1B01G053300 chr7B 94.904 157 8 0 1 157 688388428 688388584 2.940000e-61 246.0
13 TraesCS1B01G053300 chr2B 94.904 157 8 0 1 157 625067015 625067171 2.940000e-61 246.0
14 TraesCS1B01G053300 chr1A 72.632 285 59 13 727 995 22286678 22286959 4.080000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G053300 chr1B 33970046 33973854 3808 False 7035.0 7035 100.0000 1 3809 1 chr1B.!!$F2 3808
1 TraesCS1B01G053300 chr5B 572962018 572964859 2841 False 4776.0 4776 97.1500 993 3809 1 chr5B.!!$F2 2816
2 TraesCS1B01G053300 chr1D 20179279 20180162 883 True 424.5 429 86.0545 151 995 2 chr1D.!!$R1 844

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
937 998 0.107116 TACACAACCTGTTGCCGGTT 60.107 50.0 9.84 0.0 45.26 4.44 F
2294 2355 0.178981 AGGGATGCGGGATCATTTGG 60.179 55.0 11.71 0.0 31.91 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2694 2755 0.034059 CCAGCTTGGTGACGTTCTCT 59.966 55.0 1.0 0.00 31.35 3.10 R
3759 3845 0.613292 AGATCTGTCACTGACCGGCT 60.613 55.0 0.0 0.02 0.00 5.52 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
43 44 8.922738 AAAAATACACACTAATTAACACGTCG 57.077 30.769 0.00 0.00 0.00 5.12
44 45 7.872163 AAATACACACTAATTAACACGTCGA 57.128 32.000 0.00 0.00 0.00 4.20
45 46 7.502177 AATACACACTAATTAACACGTCGAG 57.498 36.000 0.00 0.00 0.00 4.04
46 47 3.671928 ACACACTAATTAACACGTCGAGC 59.328 43.478 0.00 0.00 0.00 5.03
48 49 3.165890 CACTAATTAACACGTCGAGCGA 58.834 45.455 13.06 0.00 44.77 4.93
49 50 3.237660 CACTAATTAACACGTCGAGCGAG 59.762 47.826 13.06 8.40 44.77 5.03
50 51 1.625616 AATTAACACGTCGAGCGAGG 58.374 50.000 13.06 10.58 44.77 4.63
51 52 0.806868 ATTAACACGTCGAGCGAGGA 59.193 50.000 17.92 0.00 44.77 3.71
52 53 0.167470 TTAACACGTCGAGCGAGGAG 59.833 55.000 17.92 12.83 44.77 3.69
53 54 0.671472 TAACACGTCGAGCGAGGAGA 60.671 55.000 17.92 0.00 44.77 3.71
54 55 1.512996 AACACGTCGAGCGAGGAGAA 61.513 55.000 17.92 0.00 44.77 2.87
55 56 1.209383 CACGTCGAGCGAGGAGAAA 59.791 57.895 17.92 0.00 44.77 2.52
56 57 0.386858 CACGTCGAGCGAGGAGAAAA 60.387 55.000 17.92 0.00 44.77 2.29
57 58 0.109689 ACGTCGAGCGAGGAGAAAAG 60.110 55.000 17.92 0.00 44.77 2.27
58 59 0.168348 CGTCGAGCGAGGAGAAAAGA 59.832 55.000 6.74 0.00 44.77 2.52
59 60 1.619983 GTCGAGCGAGGAGAAAAGAC 58.380 55.000 0.00 0.00 0.00 3.01
60 61 1.068472 GTCGAGCGAGGAGAAAAGACA 60.068 52.381 0.00 0.00 0.00 3.41
61 62 1.611977 TCGAGCGAGGAGAAAAGACAA 59.388 47.619 0.00 0.00 0.00 3.18
62 63 1.989165 CGAGCGAGGAGAAAAGACAAG 59.011 52.381 0.00 0.00 0.00 3.16
63 64 1.729517 GAGCGAGGAGAAAAGACAAGC 59.270 52.381 0.00 0.00 0.00 4.01
64 65 1.346068 AGCGAGGAGAAAAGACAAGCT 59.654 47.619 0.00 0.00 0.00 3.74
65 66 2.147150 GCGAGGAGAAAAGACAAGCTT 58.853 47.619 0.00 0.00 38.88 3.74
66 67 2.096019 GCGAGGAGAAAAGACAAGCTTG 60.096 50.000 24.84 24.84 36.80 4.01
67 68 2.096019 CGAGGAGAAAAGACAAGCTTGC 60.096 50.000 26.27 18.03 36.80 4.01
68 69 2.880890 GAGGAGAAAAGACAAGCTTGCA 59.119 45.455 26.27 0.00 36.80 4.08
69 70 3.290710 AGGAGAAAAGACAAGCTTGCAA 58.709 40.909 26.27 0.00 36.80 4.08
70 71 3.067320 AGGAGAAAAGACAAGCTTGCAAC 59.933 43.478 26.27 16.93 36.80 4.17
71 72 3.181487 GGAGAAAAGACAAGCTTGCAACA 60.181 43.478 26.27 0.00 36.80 3.33
72 73 4.500375 GGAGAAAAGACAAGCTTGCAACAT 60.500 41.667 26.27 10.21 36.80 2.71
73 74 5.014808 AGAAAAGACAAGCTTGCAACATT 57.985 34.783 26.27 14.46 36.80 2.71
74 75 4.807304 AGAAAAGACAAGCTTGCAACATTG 59.193 37.500 26.27 14.43 36.80 2.82
75 76 2.806608 AGACAAGCTTGCAACATTGG 57.193 45.000 26.27 0.00 0.00 3.16
76 77 1.142474 GACAAGCTTGCAACATTGGC 58.858 50.000 26.27 13.92 0.00 4.52
77 78 0.754472 ACAAGCTTGCAACATTGGCT 59.246 45.000 26.27 12.54 34.52 4.75
78 79 1.139455 ACAAGCTTGCAACATTGGCTT 59.861 42.857 26.27 15.00 42.85 4.35
79 80 2.364970 ACAAGCTTGCAACATTGGCTTA 59.635 40.909 26.27 0.00 40.60 3.09
80 81 3.181467 ACAAGCTTGCAACATTGGCTTAA 60.181 39.130 26.27 0.00 40.60 1.85
81 82 3.308438 AGCTTGCAACATTGGCTTAAG 57.692 42.857 4.42 0.00 0.00 1.85
82 83 2.629617 AGCTTGCAACATTGGCTTAAGT 59.370 40.909 4.02 0.00 0.00 2.24
83 84 3.826157 AGCTTGCAACATTGGCTTAAGTA 59.174 39.130 4.02 0.00 0.00 2.24
84 85 4.280677 AGCTTGCAACATTGGCTTAAGTAA 59.719 37.500 4.02 0.70 0.00 2.24
85 86 4.622740 GCTTGCAACATTGGCTTAAGTAAG 59.377 41.667 4.02 0.00 36.40 2.34
104 105 8.879427 AAGTAAGCATTAATTTCTACCTTGGT 57.121 30.769 0.00 0.00 34.96 3.67
105 106 9.969001 AAGTAAGCATTAATTTCTACCTTGGTA 57.031 29.630 0.00 0.00 34.96 3.25
106 107 9.392259 AGTAAGCATTAATTTCTACCTTGGTAC 57.608 33.333 0.00 0.00 28.70 3.34
107 108 7.640597 AAGCATTAATTTCTACCTTGGTACC 57.359 36.000 4.43 4.43 0.00 3.34
108 109 6.970191 AGCATTAATTTCTACCTTGGTACCT 58.030 36.000 14.36 0.00 0.00 3.08
109 110 6.828785 AGCATTAATTTCTACCTTGGTACCTG 59.171 38.462 14.36 5.99 0.00 4.00
110 111 6.602009 GCATTAATTTCTACCTTGGTACCTGT 59.398 38.462 14.36 10.21 0.00 4.00
111 112 7.771826 GCATTAATTTCTACCTTGGTACCTGTA 59.228 37.037 14.36 10.80 0.00 2.74
112 113 9.675464 CATTAATTTCTACCTTGGTACCTGTAA 57.325 33.333 14.36 0.00 0.00 2.41
116 117 9.847224 AATTTCTACCTTGGTACCTGTAATATG 57.153 33.333 14.36 1.40 0.00 1.78
117 118 6.989155 TCTACCTTGGTACCTGTAATATGG 57.011 41.667 14.36 5.80 0.00 2.74
118 119 5.842328 TCTACCTTGGTACCTGTAATATGGG 59.158 44.000 14.36 0.00 0.00 4.00
119 120 4.377134 ACCTTGGTACCTGTAATATGGGT 58.623 43.478 14.36 0.18 37.16 4.51
120 121 4.791880 ACCTTGGTACCTGTAATATGGGTT 59.208 41.667 14.36 0.00 34.86 4.11
121 122 5.254501 ACCTTGGTACCTGTAATATGGGTTT 59.745 40.000 14.36 0.00 34.86 3.27
122 123 5.592688 CCTTGGTACCTGTAATATGGGTTTG 59.407 44.000 14.36 0.00 34.86 2.93
123 124 5.782677 TGGTACCTGTAATATGGGTTTGT 57.217 39.130 14.36 0.00 34.86 2.83
124 125 5.502079 TGGTACCTGTAATATGGGTTTGTG 58.498 41.667 14.36 0.00 34.86 3.33
125 126 4.885325 GGTACCTGTAATATGGGTTTGTGG 59.115 45.833 4.06 0.00 34.86 4.17
126 127 3.361786 ACCTGTAATATGGGTTTGTGGC 58.638 45.455 0.00 0.00 0.00 5.01
127 128 2.693074 CCTGTAATATGGGTTTGTGGCC 59.307 50.000 0.00 0.00 0.00 5.36
128 129 3.627237 CCTGTAATATGGGTTTGTGGCCT 60.627 47.826 3.32 0.00 0.00 5.19
129 130 4.023291 CTGTAATATGGGTTTGTGGCCTT 58.977 43.478 3.32 0.00 0.00 4.35
130 131 3.766591 TGTAATATGGGTTTGTGGCCTTG 59.233 43.478 3.32 0.00 0.00 3.61
131 132 2.621556 ATATGGGTTTGTGGCCTTGT 57.378 45.000 3.32 0.00 0.00 3.16
132 133 3.748645 ATATGGGTTTGTGGCCTTGTA 57.251 42.857 3.32 0.00 0.00 2.41
133 134 2.621556 ATGGGTTTGTGGCCTTGTAT 57.378 45.000 3.32 0.00 0.00 2.29
134 135 3.748645 ATGGGTTTGTGGCCTTGTATA 57.251 42.857 3.32 0.00 0.00 1.47
135 136 2.797786 TGGGTTTGTGGCCTTGTATAC 58.202 47.619 3.32 0.00 0.00 1.47
136 137 2.108425 TGGGTTTGTGGCCTTGTATACA 59.892 45.455 3.32 0.08 0.00 2.29
137 138 3.158676 GGGTTTGTGGCCTTGTATACAA 58.841 45.455 17.16 17.16 0.00 2.41
138 139 3.574826 GGGTTTGTGGCCTTGTATACAAA 59.425 43.478 18.55 11.60 39.79 2.83
139 140 4.039366 GGGTTTGTGGCCTTGTATACAAAA 59.961 41.667 18.55 6.87 42.52 2.44
140 141 5.453480 GGGTTTGTGGCCTTGTATACAAAAA 60.453 40.000 18.55 12.04 42.52 1.94
141 142 6.227522 GGTTTGTGGCCTTGTATACAAAAAT 58.772 36.000 18.55 0.00 42.52 1.82
142 143 6.147000 GGTTTGTGGCCTTGTATACAAAAATG 59.853 38.462 18.55 7.55 42.52 2.32
143 144 5.398603 TGTGGCCTTGTATACAAAAATGG 57.601 39.130 18.55 16.25 35.15 3.16
144 145 5.080337 TGTGGCCTTGTATACAAAAATGGA 58.920 37.500 20.31 3.36 35.15 3.41
145 146 5.184864 TGTGGCCTTGTATACAAAAATGGAG 59.815 40.000 20.31 8.22 35.15 3.86
146 147 4.709397 TGGCCTTGTATACAAAAATGGAGG 59.291 41.667 20.31 16.09 35.15 4.30
147 148 4.099419 GGCCTTGTATACAAAAATGGAGGG 59.901 45.833 20.31 15.39 35.15 4.30
148 149 4.953579 GCCTTGTATACAAAAATGGAGGGA 59.046 41.667 20.31 0.00 35.15 4.20
149 150 5.067805 GCCTTGTATACAAAAATGGAGGGAG 59.932 44.000 20.31 5.98 35.15 4.30
179 180 4.855715 TTGGAGTGTGTTTTGTGAACAA 57.144 36.364 0.00 0.00 31.20 2.83
192 193 2.880268 TGTGAACAAAGTGCCTCTGATG 59.120 45.455 0.00 0.00 0.00 3.07
204 205 4.275936 GTGCCTCTGATGTTTGTAGTGTTT 59.724 41.667 0.00 0.00 0.00 2.83
213 214 6.601613 TGATGTTTGTAGTGTTTGGAACTTCT 59.398 34.615 0.00 0.00 0.00 2.85
214 215 6.189677 TGTTTGTAGTGTTTGGAACTTCTG 57.810 37.500 0.00 0.00 0.00 3.02
220 221 8.378172 TGTAGTGTTTGGAACTTCTGAAATAG 57.622 34.615 0.00 0.00 0.00 1.73
290 291 6.648192 ACCTGAGATTTCACAGATTTCCTAG 58.352 40.000 6.58 0.00 36.82 3.02
399 401 1.566703 TCCCCCGCCATATTTTCTTCA 59.433 47.619 0.00 0.00 0.00 3.02
433 435 3.589988 CACTACCACAGCTGAACCTAAG 58.410 50.000 23.35 11.76 0.00 2.18
434 436 2.028020 ACTACCACAGCTGAACCTAAGC 60.028 50.000 23.35 0.00 41.15 3.09
435 437 0.764890 ACCACAGCTGAACCTAAGCA 59.235 50.000 23.35 0.00 43.37 3.91
436 438 1.142870 ACCACAGCTGAACCTAAGCAA 59.857 47.619 23.35 0.00 43.37 3.91
437 439 2.229792 CCACAGCTGAACCTAAGCAAA 58.770 47.619 23.35 0.00 43.37 3.68
438 440 2.030805 CCACAGCTGAACCTAAGCAAAC 60.031 50.000 23.35 0.00 43.37 2.93
439 441 2.618241 CACAGCTGAACCTAAGCAAACA 59.382 45.455 23.35 0.00 43.37 2.83
440 442 2.618709 ACAGCTGAACCTAAGCAAACAC 59.381 45.455 23.35 0.00 43.37 3.32
441 443 2.618241 CAGCTGAACCTAAGCAAACACA 59.382 45.455 8.42 0.00 43.37 3.72
442 444 2.618709 AGCTGAACCTAAGCAAACACAC 59.381 45.455 0.00 0.00 43.37 3.82
443 445 2.357637 GCTGAACCTAAGCAAACACACA 59.642 45.455 0.00 0.00 40.52 3.72
444 446 3.548818 GCTGAACCTAAGCAAACACACAG 60.549 47.826 0.00 0.00 40.52 3.66
453 455 3.148412 AGCAAACACACAGCATACATCA 58.852 40.909 0.00 0.00 0.00 3.07
461 463 4.337274 CACACAGCATACATCAATCATGGT 59.663 41.667 0.00 0.00 36.72 3.55
466 468 8.953313 CACAGCATACATCAATCATGGTATAAT 58.047 33.333 0.00 0.00 36.72 1.28
467 469 9.524496 ACAGCATACATCAATCATGGTATAATT 57.476 29.630 0.00 0.00 36.72 1.40
518 556 3.927142 GGAACGTAACTGGACTGAGATTG 59.073 47.826 0.00 0.00 0.00 2.67
540 578 6.741992 TGGCTAGTATTCACACAAGATTTG 57.258 37.500 0.00 0.00 0.00 2.32
541 579 5.123820 TGGCTAGTATTCACACAAGATTTGC 59.876 40.000 0.00 0.00 0.00 3.68
542 580 5.449177 GGCTAGTATTCACACAAGATTTGCC 60.449 44.000 0.00 0.00 0.00 4.52
548 586 1.815003 CACACAAGATTTGCCCCTCTC 59.185 52.381 0.00 0.00 0.00 3.20
552 590 3.192212 CACAAGATTTGCCCCTCTCTTTC 59.808 47.826 0.00 0.00 0.00 2.62
576 614 9.825972 TTCTTCTCGAGCTATGTTTTAAATTTG 57.174 29.630 7.81 0.00 0.00 2.32
577 615 9.214957 TCTTCTCGAGCTATGTTTTAAATTTGA 57.785 29.630 7.81 0.00 0.00 2.69
578 616 9.483062 CTTCTCGAGCTATGTTTTAAATTTGAG 57.517 33.333 7.81 0.00 0.00 3.02
579 617 7.974675 TCTCGAGCTATGTTTTAAATTTGAGG 58.025 34.615 7.81 0.00 0.00 3.86
582 620 8.573035 TCGAGCTATGTTTTAAATTTGAGGTTT 58.427 29.630 0.00 0.00 0.00 3.27
583 621 9.191995 CGAGCTATGTTTTAAATTTGAGGTTTT 57.808 29.630 0.00 0.00 0.00 2.43
654 692 8.950208 TTTATTTTCCGGAATTTTTGAACACT 57.050 26.923 19.62 0.00 0.00 3.55
667 705 7.995463 TTTTTGAACACTTGTAAATAGTGCC 57.005 32.000 0.00 0.00 45.38 5.01
670 708 3.799432 ACACTTGTAAATAGTGCCCCA 57.201 42.857 0.00 0.00 45.38 4.96
681 732 4.899352 ATAGTGCCCCAGATATGTTCTC 57.101 45.455 0.00 0.00 29.93 2.87
705 756 0.744874 CCCGAAATACGCTCTCCAGA 59.255 55.000 0.00 0.00 41.07 3.86
709 760 3.682858 CCGAAATACGCTCTCCAGAAAAA 59.317 43.478 0.00 0.00 41.07 1.94
735 786 9.183368 AGATCATGATCCTTCTTTTTCCTTTAC 57.817 33.333 28.23 1.62 38.58 2.01
737 788 7.165485 TCATGATCCTTCTTTTTCCTTTACGA 58.835 34.615 0.00 0.00 0.00 3.43
741 792 4.060205 CCTTCTTTTTCCTTTACGACGGA 58.940 43.478 0.00 0.00 0.00 4.69
752 803 1.392589 TACGACGGATTAGGGTCCAC 58.607 55.000 0.00 0.00 38.21 4.02
769 820 0.992072 CACCTCACGTCATTACAGCG 59.008 55.000 0.00 0.00 0.00 5.18
781 832 5.234329 CGTCATTACAGCGAAGTGGAATTAT 59.766 40.000 0.00 0.00 27.49 1.28
787 838 2.679837 AGCGAAGTGGAATTATGTGCAG 59.320 45.455 0.00 0.00 0.00 4.41
789 840 3.621268 GCGAAGTGGAATTATGTGCAGTA 59.379 43.478 0.00 0.00 0.00 2.74
799 850 6.482308 GGAATTATGTGCAGTATTTACGAGGT 59.518 38.462 0.00 0.00 0.00 3.85
843 901 9.941325 TTAACCGAAACAGTAGTAATAATCCAA 57.059 29.630 0.00 0.00 0.00 3.53
847 905 6.292168 CGAAACAGTAGTAATAATCCAAGGCG 60.292 42.308 0.00 0.00 0.00 5.52
855 913 9.101655 GTAGTAATAATCCAAGGCGAAAACTAA 57.898 33.333 0.00 0.00 0.00 2.24
857 915 9.185680 AGTAATAATCCAAGGCGAAAACTAATT 57.814 29.630 0.00 0.00 0.00 1.40
888 946 3.382546 CACCAATGGATAAAGAAGGCCAG 59.617 47.826 6.16 0.00 33.26 4.85
889 947 3.011708 ACCAATGGATAAAGAAGGCCAGT 59.988 43.478 6.16 0.00 33.26 4.00
892 950 3.634397 TGGATAAAGAAGGCCAGTGAG 57.366 47.619 5.01 0.00 0.00 3.51
905 963 3.304928 GGCCAGTGAGATTTGACAAACAG 60.305 47.826 1.94 0.00 0.00 3.16
912 973 7.377928 CAGTGAGATTTGACAAACAGAAATCAC 59.622 37.037 1.94 10.63 31.72 3.06
925 986 6.545504 ACAGAAATCACTGTCATACACAAC 57.454 37.500 0.00 0.00 46.36 3.32
933 994 2.226330 TGTCATACACAACCTGTTGCC 58.774 47.619 9.84 0.00 44.03 4.52
935 996 0.521291 CATACACAACCTGTTGCCGG 59.479 55.000 9.84 0.00 44.03 6.13
936 997 0.109723 ATACACAACCTGTTGCCGGT 59.890 50.000 9.84 8.43 44.03 5.28
937 998 0.107116 TACACAACCTGTTGCCGGTT 60.107 50.000 9.84 0.00 45.26 4.44
940 1001 3.223589 AACCTGTTGCCGGTTGCC 61.224 61.111 1.90 0.00 42.87 4.52
943 1004 3.365265 CTGTTGCCGGTTGCCCTC 61.365 66.667 1.90 0.00 40.16 4.30
949 1010 4.003788 CCGGTTGCCCTCACGAGT 62.004 66.667 0.00 0.00 0.00 4.18
950 1011 2.738521 CGGTTGCCCTCACGAGTG 60.739 66.667 0.00 0.00 0.00 3.51
951 1012 2.741092 GGTTGCCCTCACGAGTGA 59.259 61.111 5.76 5.76 38.06 3.41
952 1013 1.296715 GGTTGCCCTCACGAGTGAT 59.703 57.895 6.37 0.00 39.13 3.06
953 1014 0.741221 GGTTGCCCTCACGAGTGATC 60.741 60.000 6.37 0.73 39.13 2.92
954 1015 0.741221 GTTGCCCTCACGAGTGATCC 60.741 60.000 6.37 0.00 39.13 3.36
967 1028 4.097892 ACGAGTGATCCAAACTTGCTTTTT 59.902 37.500 0.00 0.00 33.03 1.94
979 1040 7.759433 CCAAACTTGCTTTTTGAGAAAGAGTTA 59.241 33.333 0.00 0.00 42.88 2.24
987 1048 8.184848 GCTTTTTGAGAAAGAGTTAAGTCACTT 58.815 33.333 12.77 0.00 0.00 3.16
1001 1062 5.559148 AAGTCACTTTCAGAGAGGAACAT 57.441 39.130 0.00 0.00 0.00 2.71
1069 1130 1.649664 CCGAGCCTCAGACTTCAATG 58.350 55.000 0.00 0.00 0.00 2.82
1093 1154 5.760253 GTGATCCATCGTCCTGATATTGTTT 59.240 40.000 0.00 0.00 34.83 2.83
1254 1315 0.240945 GCACATACACACACAAGGGC 59.759 55.000 0.00 0.00 0.00 5.19
1296 1357 1.229464 AGAGGGCAGAACCAGAGCT 60.229 57.895 0.00 0.00 42.05 4.09
1460 1521 1.973515 CAGGGATACTGCTGCCTATGA 59.026 52.381 0.00 0.00 40.97 2.15
1539 1600 3.262420 CATTTGTCTCCCGTTAGAGGTG 58.738 50.000 0.00 0.00 34.46 4.00
1595 1656 2.320587 GCCCGACAGCACAAGACAG 61.321 63.158 0.00 0.00 0.00 3.51
1668 1729 1.961180 CTAGGGAACAGGCCGACCAG 61.961 65.000 0.00 0.00 39.06 4.00
1808 1869 2.116983 TTGCCACCTCAGGAGCTCAC 62.117 60.000 17.19 5.01 0.00 3.51
1863 1924 2.044450 AAGGAGGCTGGGGGCATA 59.956 61.111 0.00 0.00 44.01 3.14
2035 2096 0.543277 CAGCTATGAGTTGCCTCCCA 59.457 55.000 0.00 0.00 36.86 4.37
2115 2176 4.864334 GCGATGGCCTGGGACCTG 62.864 72.222 3.32 0.00 0.00 4.00
2119 2180 3.658346 ATGGCCTGGGACCTGCCTA 62.658 63.158 18.68 9.28 45.56 3.93
2208 2269 0.474184 CTGGACCTGAGGTGGTGTTT 59.526 55.000 9.89 0.00 41.00 2.83
2256 2317 2.074948 CCATCCCCCTCCTGGACTG 61.075 68.421 0.00 0.00 33.94 3.51
2283 2344 1.871408 GCTGATAGACACAGGGATGCG 60.871 57.143 0.00 0.00 36.09 4.73
2284 2345 0.752658 TGATAGACACAGGGATGCGG 59.247 55.000 0.00 0.00 0.00 5.69
2294 2355 0.178981 AGGGATGCGGGATCATTTGG 60.179 55.000 11.71 0.00 31.91 3.28
2386 2447 2.125552 CAGCGATCACGGCAAGGA 60.126 61.111 0.00 0.00 40.15 3.36
2437 2498 4.083696 GGCAGTTCATTGGAAAAATTGCTG 60.084 41.667 0.00 0.00 34.13 4.41
2444 2505 2.328319 TGGAAAAATTGCTGCCCTCTT 58.672 42.857 0.00 0.00 0.00 2.85
2499 2560 2.435586 CCCTCACCTCGCAAGCTG 60.436 66.667 0.00 0.00 37.18 4.24
2623 2684 0.443869 CGTCAAGCTGGGTTTCATCG 59.556 55.000 0.00 0.00 0.00 3.84
2762 2823 2.886124 GCTACAGCTTCCGGACGC 60.886 66.667 24.53 24.53 38.21 5.19
2830 2891 2.154462 CTTCCTTCGTTTGACCATGCT 58.846 47.619 0.00 0.00 0.00 3.79
2870 2931 6.089249 AGTTTCCAATGATTTGTTGTCCTC 57.911 37.500 0.00 0.00 0.00 3.71
2894 2955 5.757988 TGAACCTTAAGTTTACTGTTGGGT 58.242 37.500 0.97 0.00 39.40 4.51
2931 3017 3.877559 TGTATCCTGCTTGATCTTGTGG 58.122 45.455 0.00 0.00 0.00 4.17
3009 3095 1.798813 GTTGAATAATAGGGCGAGGCG 59.201 52.381 0.00 0.00 0.00 5.52
3368 3454 3.802139 CGATATTCATAACACCGTGCAGT 59.198 43.478 0.00 0.00 0.00 4.40
3395 3481 6.454795 CCATGGTTAATTATTGGGGATTTCG 58.545 40.000 2.57 0.00 0.00 3.46
3464 3550 4.062293 TCGATGGATGAACAAGTTTCGTT 58.938 39.130 3.40 0.00 0.00 3.85
3541 3627 3.344515 GTGGAGTAATGAACAAGACCCC 58.655 50.000 0.00 0.00 0.00 4.95
3573 3659 2.949451 AGACTAGACCGTGCATTCTG 57.051 50.000 0.00 0.00 0.00 3.02
3660 3746 2.103143 CTGTCCGCTACTGCTCCG 59.897 66.667 0.00 0.00 36.97 4.63
3727 3813 4.410099 CATATTGGCAATATGTCCAGGGT 58.590 43.478 35.78 13.31 43.60 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.763356 TCGACGTGTTAATTAGTGTGTATTTTT 58.237 29.630 0.00 0.00 0.00 1.94
19 20 8.296799 TCGACGTGTTAATTAGTGTGTATTTT 57.703 30.769 0.00 0.00 0.00 1.82
20 21 7.411157 GCTCGACGTGTTAATTAGTGTGTATTT 60.411 37.037 0.00 0.00 0.00 1.40
21 22 6.034256 GCTCGACGTGTTAATTAGTGTGTATT 59.966 38.462 0.00 0.00 0.00 1.89
22 23 5.514204 GCTCGACGTGTTAATTAGTGTGTAT 59.486 40.000 0.00 0.00 0.00 2.29
23 24 4.853196 GCTCGACGTGTTAATTAGTGTGTA 59.147 41.667 0.00 0.00 0.00 2.90
24 25 3.671928 GCTCGACGTGTTAATTAGTGTGT 59.328 43.478 0.00 0.00 0.00 3.72
25 26 3.241239 CGCTCGACGTGTTAATTAGTGTG 60.241 47.826 0.00 0.00 36.87 3.82
26 27 2.912967 CGCTCGACGTGTTAATTAGTGT 59.087 45.455 0.00 0.00 36.87 3.55
27 28 3.165890 TCGCTCGACGTGTTAATTAGTG 58.834 45.455 0.00 0.00 44.19 2.74
28 29 3.423571 CTCGCTCGACGTGTTAATTAGT 58.576 45.455 0.00 0.00 44.19 2.24
29 30 2.782192 CCTCGCTCGACGTGTTAATTAG 59.218 50.000 0.00 0.00 44.19 1.73
30 31 2.419673 TCCTCGCTCGACGTGTTAATTA 59.580 45.455 0.00 0.00 44.19 1.40
31 32 1.200716 TCCTCGCTCGACGTGTTAATT 59.799 47.619 0.00 0.00 44.19 1.40
32 33 0.806868 TCCTCGCTCGACGTGTTAAT 59.193 50.000 0.00 0.00 44.19 1.40
33 34 0.167470 CTCCTCGCTCGACGTGTTAA 59.833 55.000 0.00 0.00 44.19 2.01
34 35 0.671472 TCTCCTCGCTCGACGTGTTA 60.671 55.000 0.00 0.00 44.19 2.41
35 36 1.512996 TTCTCCTCGCTCGACGTGTT 61.513 55.000 0.00 0.00 44.19 3.32
36 37 1.512996 TTTCTCCTCGCTCGACGTGT 61.513 55.000 0.00 0.00 44.19 4.49
37 38 0.386858 TTTTCTCCTCGCTCGACGTG 60.387 55.000 0.00 0.00 44.19 4.49
38 39 0.109689 CTTTTCTCCTCGCTCGACGT 60.110 55.000 0.00 0.00 44.19 4.34
39 40 0.168348 TCTTTTCTCCTCGCTCGACG 59.832 55.000 0.00 0.00 45.62 5.12
40 41 1.068472 TGTCTTTTCTCCTCGCTCGAC 60.068 52.381 0.00 0.00 0.00 4.20
41 42 1.244816 TGTCTTTTCTCCTCGCTCGA 58.755 50.000 0.00 0.00 0.00 4.04
42 43 1.989165 CTTGTCTTTTCTCCTCGCTCG 59.011 52.381 0.00 0.00 0.00 5.03
43 44 1.729517 GCTTGTCTTTTCTCCTCGCTC 59.270 52.381 0.00 0.00 0.00 5.03
44 45 1.346068 AGCTTGTCTTTTCTCCTCGCT 59.654 47.619 0.00 0.00 0.00 4.93
45 46 1.802069 AGCTTGTCTTTTCTCCTCGC 58.198 50.000 0.00 0.00 0.00 5.03
46 47 2.096019 GCAAGCTTGTCTTTTCTCCTCG 60.096 50.000 26.55 0.00 31.27 4.63
47 48 2.880890 TGCAAGCTTGTCTTTTCTCCTC 59.119 45.455 26.55 6.81 31.27 3.71
48 49 2.936202 TGCAAGCTTGTCTTTTCTCCT 58.064 42.857 26.55 0.00 31.27 3.69
49 50 3.181487 TGTTGCAAGCTTGTCTTTTCTCC 60.181 43.478 26.55 8.02 31.27 3.71
50 51 4.032703 TGTTGCAAGCTTGTCTTTTCTC 57.967 40.909 26.55 8.72 31.27 2.87
51 52 4.660789 ATGTTGCAAGCTTGTCTTTTCT 57.339 36.364 26.55 4.54 31.27 2.52
52 53 4.025480 CCAATGTTGCAAGCTTGTCTTTTC 60.025 41.667 26.55 10.14 31.27 2.29
53 54 3.872771 CCAATGTTGCAAGCTTGTCTTTT 59.127 39.130 26.55 12.00 31.27 2.27
54 55 3.460103 CCAATGTTGCAAGCTTGTCTTT 58.540 40.909 26.55 17.10 31.27 2.52
55 56 2.804212 GCCAATGTTGCAAGCTTGTCTT 60.804 45.455 26.55 12.91 34.78 3.01
56 57 1.269936 GCCAATGTTGCAAGCTTGTCT 60.270 47.619 26.55 5.56 0.00 3.41
57 58 1.142474 GCCAATGTTGCAAGCTTGTC 58.858 50.000 26.55 18.78 0.00 3.18
58 59 0.754472 AGCCAATGTTGCAAGCTTGT 59.246 45.000 26.55 4.42 0.00 3.16
59 60 1.873698 AAGCCAATGTTGCAAGCTTG 58.126 45.000 22.44 22.44 41.97 4.01
60 61 3.070015 ACTTAAGCCAATGTTGCAAGCTT 59.930 39.130 21.82 21.82 45.27 3.74
61 62 2.629617 ACTTAAGCCAATGTTGCAAGCT 59.370 40.909 0.00 0.96 34.64 3.74
62 63 3.030668 ACTTAAGCCAATGTTGCAAGC 57.969 42.857 0.00 0.00 0.00 4.01
78 79 9.969001 ACCAAGGTAGAAATTAATGCTTACTTA 57.031 29.630 0.00 0.00 0.00 2.24
79 80 8.879427 ACCAAGGTAGAAATTAATGCTTACTT 57.121 30.769 0.00 0.00 0.00 2.24
80 81 9.392259 GTACCAAGGTAGAAATTAATGCTTACT 57.608 33.333 0.00 0.00 0.00 2.24
81 82 8.618677 GGTACCAAGGTAGAAATTAATGCTTAC 58.381 37.037 7.15 0.00 0.00 2.34
82 83 8.554011 AGGTACCAAGGTAGAAATTAATGCTTA 58.446 33.333 15.94 0.00 0.00 3.09
83 84 7.339466 CAGGTACCAAGGTAGAAATTAATGCTT 59.661 37.037 15.94 0.00 0.00 3.91
84 85 6.828785 CAGGTACCAAGGTAGAAATTAATGCT 59.171 38.462 15.94 0.00 0.00 3.79
85 86 6.602009 ACAGGTACCAAGGTAGAAATTAATGC 59.398 38.462 15.94 0.00 0.00 3.56
86 87 9.675464 TTACAGGTACCAAGGTAGAAATTAATG 57.325 33.333 15.94 0.00 0.00 1.90
90 91 9.847224 CATATTACAGGTACCAAGGTAGAAATT 57.153 33.333 15.94 1.40 0.00 1.82
91 92 8.437575 CCATATTACAGGTACCAAGGTAGAAAT 58.562 37.037 15.94 8.47 0.00 2.17
92 93 7.147444 CCCATATTACAGGTACCAAGGTAGAAA 60.147 40.741 15.94 1.52 0.00 2.52
93 94 6.328148 CCCATATTACAGGTACCAAGGTAGAA 59.672 42.308 15.94 6.06 0.00 2.10
94 95 5.842328 CCCATATTACAGGTACCAAGGTAGA 59.158 44.000 15.94 6.19 0.00 2.59
95 96 5.605488 ACCCATATTACAGGTACCAAGGTAG 59.395 44.000 15.94 3.65 30.13 3.18
96 97 5.540808 ACCCATATTACAGGTACCAAGGTA 58.459 41.667 15.94 10.60 30.13 3.08
97 98 4.377134 ACCCATATTACAGGTACCAAGGT 58.623 43.478 15.94 11.64 30.13 3.50
98 99 5.382664 AACCCATATTACAGGTACCAAGG 57.617 43.478 15.94 5.66 32.21 3.61
99 100 6.094881 CACAAACCCATATTACAGGTACCAAG 59.905 42.308 15.94 8.83 32.21 3.61
100 101 5.946972 CACAAACCCATATTACAGGTACCAA 59.053 40.000 15.94 0.00 32.21 3.67
101 102 5.502079 CACAAACCCATATTACAGGTACCA 58.498 41.667 15.94 0.00 32.21 3.25
102 103 4.885325 CCACAAACCCATATTACAGGTACC 59.115 45.833 2.73 2.73 32.21 3.34
103 104 4.337274 GCCACAAACCCATATTACAGGTAC 59.663 45.833 0.00 0.00 32.21 3.34
104 105 4.528920 GCCACAAACCCATATTACAGGTA 58.471 43.478 0.00 0.00 32.21 3.08
105 106 3.361786 GCCACAAACCCATATTACAGGT 58.638 45.455 0.00 0.00 34.60 4.00
106 107 2.693074 GGCCACAAACCCATATTACAGG 59.307 50.000 0.00 0.00 0.00 4.00
107 108 3.631250 AGGCCACAAACCCATATTACAG 58.369 45.455 5.01 0.00 0.00 2.74
108 109 3.748645 AGGCCACAAACCCATATTACA 57.251 42.857 5.01 0.00 0.00 2.41
109 110 3.767131 ACAAGGCCACAAACCCATATTAC 59.233 43.478 5.01 0.00 0.00 1.89
110 111 4.054359 ACAAGGCCACAAACCCATATTA 57.946 40.909 5.01 0.00 0.00 0.98
111 112 2.901291 ACAAGGCCACAAACCCATATT 58.099 42.857 5.01 0.00 0.00 1.28
112 113 2.621556 ACAAGGCCACAAACCCATAT 57.378 45.000 5.01 0.00 0.00 1.78
113 114 3.748645 ATACAAGGCCACAAACCCATA 57.251 42.857 5.01 0.00 0.00 2.74
114 115 2.621556 ATACAAGGCCACAAACCCAT 57.378 45.000 5.01 0.00 0.00 4.00
115 116 2.108425 TGTATACAAGGCCACAAACCCA 59.892 45.455 5.01 0.00 0.00 4.51
116 117 2.797786 TGTATACAAGGCCACAAACCC 58.202 47.619 5.01 0.00 0.00 4.11
117 118 4.857509 TTTGTATACAAGGCCACAAACC 57.142 40.909 17.36 0.00 36.31 3.27
118 119 6.147000 CCATTTTTGTATACAAGGCCACAAAC 59.853 38.462 17.36 1.89 39.78 2.93
119 120 6.042093 TCCATTTTTGTATACAAGGCCACAAA 59.958 34.615 17.36 13.98 38.68 2.83
120 121 5.540337 TCCATTTTTGTATACAAGGCCACAA 59.460 36.000 17.36 2.10 37.15 3.33
121 122 5.080337 TCCATTTTTGTATACAAGGCCACA 58.920 37.500 17.36 0.00 37.15 4.17
122 123 5.394115 CCTCCATTTTTGTATACAAGGCCAC 60.394 44.000 17.36 0.00 37.15 5.01
123 124 4.709397 CCTCCATTTTTGTATACAAGGCCA 59.291 41.667 17.36 1.16 37.15 5.36
124 125 4.099419 CCCTCCATTTTTGTATACAAGGCC 59.901 45.833 17.36 0.00 37.15 5.19
125 126 4.953579 TCCCTCCATTTTTGTATACAAGGC 59.046 41.667 17.36 0.00 37.15 4.35
126 127 6.187682 ACTCCCTCCATTTTTGTATACAAGG 58.812 40.000 17.36 15.00 37.15 3.61
127 128 8.980481 ATACTCCCTCCATTTTTGTATACAAG 57.020 34.615 17.36 6.89 37.15 3.16
162 163 3.987220 GCACTTTGTTCACAAAACACACT 59.013 39.130 6.57 0.00 44.24 3.55
171 172 2.708216 TCAGAGGCACTTTGTTCACA 57.292 45.000 0.00 0.00 41.71 3.58
179 180 4.067896 CACTACAAACATCAGAGGCACTT 58.932 43.478 0.00 0.00 41.55 3.16
192 193 6.431198 TCAGAAGTTCCAAACACTACAAAC 57.569 37.500 0.00 0.00 0.00 2.93
204 205 8.156820 TGACTTGAATCTATTTCAGAAGTTCCA 58.843 33.333 0.00 0.00 44.90 3.53
267 268 6.760770 GTCTAGGAAATCTGTGAAATCTCAGG 59.239 42.308 11.37 0.00 37.87 3.86
317 318 6.394025 AAGTTGGCTTACATAACGGAAAAA 57.606 33.333 0.00 0.00 32.27 1.94
363 364 3.119495 CGGGGGACAAATTCTTGTGATTC 60.119 47.826 0.00 0.00 45.98 2.52
399 401 5.648092 GCTGTGGTAGTGGATAAACAGAAAT 59.352 40.000 4.87 0.00 34.44 2.17
433 435 3.557577 TGATGTATGCTGTGTGTTTGC 57.442 42.857 0.00 0.00 0.00 3.68
434 436 5.701855 TGATTGATGTATGCTGTGTGTTTG 58.298 37.500 0.00 0.00 0.00 2.93
435 437 5.963176 TGATTGATGTATGCTGTGTGTTT 57.037 34.783 0.00 0.00 0.00 2.83
436 438 5.163591 CCATGATTGATGTATGCTGTGTGTT 60.164 40.000 0.00 0.00 0.00 3.32
437 439 4.337274 CCATGATTGATGTATGCTGTGTGT 59.663 41.667 0.00 0.00 0.00 3.72
438 440 4.337274 ACCATGATTGATGTATGCTGTGTG 59.663 41.667 0.00 0.00 0.00 3.82
439 441 4.529897 ACCATGATTGATGTATGCTGTGT 58.470 39.130 0.00 0.00 0.00 3.72
440 442 6.812879 ATACCATGATTGATGTATGCTGTG 57.187 37.500 0.00 0.00 0.00 3.66
441 443 9.524496 AATTATACCATGATTGATGTATGCTGT 57.476 29.630 0.00 0.00 0.00 4.40
476 478 6.745450 CGTTCCGTTTTTCATGCTATGTTATT 59.255 34.615 0.00 0.00 0.00 1.40
502 504 4.353777 ACTAGCCAATCTCAGTCCAGTTA 58.646 43.478 0.00 0.00 0.00 2.24
504 506 2.826488 ACTAGCCAATCTCAGTCCAGT 58.174 47.619 0.00 0.00 0.00 4.00
506 508 4.962362 TGAATACTAGCCAATCTCAGTCCA 59.038 41.667 0.00 0.00 0.00 4.02
507 509 5.163405 TGTGAATACTAGCCAATCTCAGTCC 60.163 44.000 0.00 0.00 0.00 3.85
510 548 5.664457 TGTGTGAATACTAGCCAATCTCAG 58.336 41.667 0.00 0.00 0.00 3.35
513 551 6.299805 TCTTGTGTGAATACTAGCCAATCT 57.700 37.500 0.00 0.00 0.00 2.40
518 556 5.449177 GGCAAATCTTGTGTGAATACTAGCC 60.449 44.000 0.00 0.00 0.00 3.93
540 578 1.136110 CTCGAGAAGAAAGAGAGGGGC 59.864 57.143 6.58 0.00 34.13 5.80
541 579 1.136110 GCTCGAGAAGAAAGAGAGGGG 59.864 57.143 18.75 0.00 34.13 4.79
542 580 2.099405 AGCTCGAGAAGAAAGAGAGGG 58.901 52.381 18.75 0.00 34.13 4.30
552 590 9.483062 CTCAAATTTAAAACATAGCTCGAGAAG 57.517 33.333 18.75 4.42 0.00 2.85
575 613 7.432838 GCAAACGTTACAAGATTAAAAACCTCA 59.567 33.333 0.00 0.00 0.00 3.86
576 614 7.432838 TGCAAACGTTACAAGATTAAAAACCTC 59.567 33.333 0.00 0.00 0.00 3.85
577 615 7.259161 TGCAAACGTTACAAGATTAAAAACCT 58.741 30.769 0.00 0.00 0.00 3.50
578 616 7.432838 TCTGCAAACGTTACAAGATTAAAAACC 59.567 33.333 0.00 0.00 0.00 3.27
579 617 8.330302 TCTGCAAACGTTACAAGATTAAAAAC 57.670 30.769 0.00 0.00 0.00 2.43
584 622 9.767684 CATATTTCTGCAAACGTTACAAGATTA 57.232 29.630 0.00 1.42 0.00 1.75
631 669 7.982354 ACAAGTGTTCAAAAATTCCGGAAAATA 59.018 29.630 23.08 5.14 0.00 1.40
632 670 6.821160 ACAAGTGTTCAAAAATTCCGGAAAAT 59.179 30.769 23.08 10.70 0.00 1.82
637 675 7.707774 ATTTACAAGTGTTCAAAAATTCCGG 57.292 32.000 0.00 0.00 0.00 5.14
654 692 6.260700 ACATATCTGGGGCACTATTTACAA 57.739 37.500 0.00 0.00 0.00 2.41
689 740 6.313905 TGATCTTTTTCTGGAGAGCGTATTTC 59.686 38.462 0.00 0.00 31.20 2.17
709 760 9.183368 GTAAAGGAAAAAGAAGGATCATGATCT 57.817 33.333 29.85 15.27 37.92 2.75
729 780 2.223900 GGACCCTAATCCGTCGTAAAGG 60.224 54.545 0.00 0.00 0.00 3.11
735 786 1.041447 AGGTGGACCCTAATCCGTCG 61.041 60.000 0.00 0.00 43.87 5.12
737 788 0.042131 TGAGGTGGACCCTAATCCGT 59.958 55.000 0.00 0.00 46.51 4.69
741 792 1.192428 GACGTGAGGTGGACCCTAAT 58.808 55.000 0.00 0.00 46.51 1.73
752 803 1.920574 CTTCGCTGTAATGACGTGAGG 59.079 52.381 0.00 0.00 0.00 3.86
758 809 4.946784 AATTCCACTTCGCTGTAATGAC 57.053 40.909 0.00 0.00 0.00 3.06
769 820 7.850982 CGTAAATACTGCACATAATTCCACTTC 59.149 37.037 0.00 0.00 0.00 3.01
781 832 3.581755 GACACCTCGTAAATACTGCACA 58.418 45.455 0.00 0.00 0.00 4.57
787 838 2.850647 GCTGTCGACACCTCGTAAATAC 59.149 50.000 15.76 0.00 41.02 1.89
789 840 1.403780 GGCTGTCGACACCTCGTAAAT 60.404 52.381 15.76 0.00 41.02 1.40
828 879 7.336396 AGTTTTCGCCTTGGATTATTACTACT 58.664 34.615 0.00 0.00 0.00 2.57
857 915 1.739750 ATCCATTGGTGGGGCAAAAA 58.260 45.000 1.86 0.00 46.06 1.94
867 925 3.011708 ACTGGCCTTCTTTATCCATTGGT 59.988 43.478 3.32 0.00 0.00 3.67
877 935 3.823304 GTCAAATCTCACTGGCCTTCTTT 59.177 43.478 3.32 0.00 0.00 2.52
886 944 7.377928 GTGATTTCTGTTTGTCAAATCTCACTG 59.622 37.037 0.40 0.00 0.00 3.66
888 946 7.377928 CAGTGATTTCTGTTTGTCAAATCTCAC 59.622 37.037 0.40 8.42 0.00 3.51
889 947 7.067372 ACAGTGATTTCTGTTTGTCAAATCTCA 59.933 33.333 0.40 0.00 44.92 3.27
892 950 7.195646 TGACAGTGATTTCTGTTTGTCAAATC 58.804 34.615 0.40 0.00 46.81 2.17
905 963 5.470098 ACAGGTTGTGTATGACAGTGATTTC 59.530 40.000 0.00 0.00 37.75 2.17
912 973 2.226437 GGCAACAGGTTGTGTATGACAG 59.774 50.000 13.19 0.00 39.03 3.51
919 980 1.379309 AACCGGCAACAGGTTGTGT 60.379 52.632 13.19 6.25 46.67 3.72
920 981 3.520402 AACCGGCAACAGGTTGTG 58.480 55.556 13.19 6.76 46.67 3.33
935 996 0.741221 GGATCACTCGTGAGGGCAAC 60.741 60.000 5.91 0.00 43.61 4.17
936 997 1.191489 TGGATCACTCGTGAGGGCAA 61.191 55.000 5.91 0.00 43.61 4.52
937 998 1.191489 TTGGATCACTCGTGAGGGCA 61.191 55.000 5.91 0.00 43.61 5.36
938 999 0.036388 TTTGGATCACTCGTGAGGGC 60.036 55.000 5.91 0.00 43.61 5.19
939 1000 1.276421 AGTTTGGATCACTCGTGAGGG 59.724 52.381 5.91 0.00 43.61 4.30
940 1001 2.738846 CAAGTTTGGATCACTCGTGAGG 59.261 50.000 5.91 0.00 43.61 3.86
941 1002 2.158449 GCAAGTTTGGATCACTCGTGAG 59.842 50.000 5.91 0.00 43.61 3.51
943 1004 2.146342 AGCAAGTTTGGATCACTCGTG 58.854 47.619 0.00 0.00 0.00 4.35
946 1007 5.591099 TCAAAAAGCAAGTTTGGATCACTC 58.409 37.500 0.00 0.00 36.75 3.51
948 1009 5.591099 TCTCAAAAAGCAAGTTTGGATCAC 58.409 37.500 0.00 0.00 36.75 3.06
949 1010 5.850557 TCTCAAAAAGCAAGTTTGGATCA 57.149 34.783 0.00 0.00 36.75 2.92
950 1011 6.980397 TCTTTCTCAAAAAGCAAGTTTGGATC 59.020 34.615 6.85 0.00 36.75 3.36
951 1012 6.877236 TCTTTCTCAAAAAGCAAGTTTGGAT 58.123 32.000 6.85 0.00 36.75 3.41
952 1013 6.071391 ACTCTTTCTCAAAAAGCAAGTTTGGA 60.071 34.615 6.85 0.00 36.75 3.53
953 1014 6.101997 ACTCTTTCTCAAAAAGCAAGTTTGG 58.898 36.000 6.85 0.00 36.75 3.28
954 1015 7.586714 AACTCTTTCTCAAAAAGCAAGTTTG 57.413 32.000 0.00 0.00 37.32 2.93
967 1028 7.782049 TCTGAAAGTGACTTAACTCTTTCTCA 58.218 34.615 17.56 0.00 44.02 3.27
979 1040 5.163258 ACATGTTCCTCTCTGAAAGTGACTT 60.163 40.000 0.00 0.00 32.32 3.01
987 1048 2.353109 CGCTGACATGTTCCTCTCTGAA 60.353 50.000 0.00 0.00 0.00 3.02
1069 1130 4.887748 ACAATATCAGGACGATGGATCAC 58.112 43.478 0.00 0.00 35.39 3.06
1254 1315 0.254178 CCTTCACACCCATCCTCCAG 59.746 60.000 0.00 0.00 0.00 3.86
1582 1643 1.128200 TACACCCTGTCTTGTGCTGT 58.872 50.000 0.00 0.00 35.90 4.40
1668 1729 2.385237 CTCATCTGTGAGCTGCTGC 58.615 57.895 7.01 7.62 44.86 5.25
1829 1890 2.978978 TCCTTCTCCATCACAAGGACAA 59.021 45.455 0.00 0.00 40.70 3.18
1995 2056 2.338500 GTACGTTGCTGGAAGAAGGAG 58.662 52.381 0.00 0.00 34.07 3.69
2035 2096 1.078426 CGTCCAAAGAAGGCGGGAT 60.078 57.895 0.00 0.00 0.00 3.85
2256 2317 0.173481 TGTGTCTATCAGCGCAGTCC 59.827 55.000 11.47 0.00 0.00 3.85
2283 2344 2.158914 GGATTGTTGGCCAAATGATCCC 60.159 50.000 29.02 19.34 36.44 3.85
2284 2345 2.500910 TGGATTGTTGGCCAAATGATCC 59.499 45.455 30.79 30.79 36.44 3.36
2294 2355 1.303309 CTCCTCGATGGATTGTTGGC 58.697 55.000 4.39 0.00 45.16 4.52
2314 2375 4.467062 TGCTCGTCTCGCTCGCTG 62.467 66.667 0.00 0.00 0.00 5.18
2386 2447 1.207488 TCCAGGTGTAAGGCAGCCAT 61.207 55.000 15.80 3.67 46.08 4.40
2437 2498 0.985490 ATGGAGGAGGACAAGAGGGC 60.985 60.000 0.00 0.00 0.00 5.19
2444 2505 0.105453 GCCTAGGATGGAGGAGGACA 60.105 60.000 14.75 0.00 35.99 4.02
2499 2560 1.221021 CCCCAGTAGGCGGTTCTTC 59.779 63.158 0.00 0.00 0.00 2.87
2613 2674 1.376812 AGGGCGTTCGATGAAACCC 60.377 57.895 9.74 9.74 39.25 4.11
2623 2684 2.412847 CGTTGAAATCTTCAGGGCGTTC 60.413 50.000 0.00 0.00 41.38 3.95
2694 2755 0.034059 CCAGCTTGGTGACGTTCTCT 59.966 55.000 1.00 0.00 31.35 3.10
2762 2823 3.267860 GGATCGCTTGCAGCTCGG 61.268 66.667 0.00 0.00 39.60 4.63
2870 2931 5.826208 ACCCAACAGTAAACTTAAGGTTCAG 59.174 40.000 9.55 3.61 37.12 3.02
3192 3278 1.573436 GCAGCAGACACACAGAAGC 59.427 57.895 0.00 0.00 0.00 3.86
3300 3386 2.102553 GCTCGTAGTCGTGAGGGC 59.897 66.667 0.00 0.00 38.33 5.19
3368 3454 3.051803 TCCCCAATAATTAACCATGGCCA 60.052 43.478 13.04 8.56 0.00 5.36
3395 3481 5.741962 TCTCTTGGATCCATGATCAGATC 57.258 43.478 25.92 13.90 40.50 2.75
3464 3550 8.595362 TGGAGACTTGATCTATTAAGAGTTCA 57.405 34.615 6.75 6.75 38.00 3.18
3541 3627 3.066481 GGTCTAGTCTAACTAGCGTTGGG 59.934 52.174 8.89 0.00 45.93 4.12
3573 3659 1.820519 TGAGCTCCCAATCAACATTGC 59.179 47.619 12.15 0.00 38.53 3.56
3649 3735 1.516603 GTCGTTCCGGAGCAGTAGC 60.517 63.158 19.03 0.00 42.56 3.58
3660 3746 5.773239 TGTTTTGATTATCTCGTCGTTCC 57.227 39.130 0.00 0.00 0.00 3.62
3727 3813 1.695242 TGCTGGACGACCTCCTTAAAA 59.305 47.619 5.33 0.00 40.26 1.52
3759 3845 0.613292 AGATCTGTCACTGACCGGCT 60.613 55.000 0.00 0.02 0.00 5.52
3769 3855 3.176411 ACTTGTGATGGGAGATCTGTCA 58.824 45.455 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.