Multiple sequence alignment - TraesCS1D01G352700

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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 TraesCS1D01G352700 chr1D 100.000 3610 0 0 1 3610 438259754 438256145 0.000000e+00 6667
1 TraesCS1D01G352700 chr1D 93.730 638 31 4 2982 3610 478398817 478398180 0.000000e+00 948
2 TraesCS1D01G352700 chr1A 87.123 2586 160 101 167 2663 534943668 534941167 0.000000e+00 2771
3 TraesCS1D01G352700 chr1A 92.013 313 22 3 2662 2973 534941088 534940778 1.540000e-118 436
4 TraesCS1D01G352700 chr1B 86.595 2596 193 89 166 2658 593891912 593889369 0.000000e+00 2723
5 TraesCS1D01G352700 chr1B 91.593 226 12 3 2662 2881 593889292 593889068 4.530000e-79 305
6 TraesCS1D01G352700 chr1B 94.737 76 4 0 2908 2983 593889072 593888997 6.330000e-23 119
7 TraesCS1D01G352700 chr5B 94.192 637 28 4 2983 3610 243414648 243414012 0.000000e+00 963
8 TraesCS1D01G352700 chr5B 92.767 636 35 5 2984 3610 282019195 282018562 0.000000e+00 909
9 TraesCS1D01G352700 chr2D 93.887 638 29 4 2983 3610 446308472 446309109 0.000000e+00 953
10 TraesCS1D01G352700 chr2D 93.292 641 33 4 2979 3610 619422543 619423182 0.000000e+00 937
11 TraesCS1D01G352700 chr7B 92.679 642 37 4 2977 3608 746376199 746375558 0.000000e+00 917
12 TraesCS1D01G352700 chr7B 92.441 635 40 5 2984 3610 606064794 606065428 0.000000e+00 900
13 TraesCS1D01G352700 chr4B 92.756 635 38 7 2984 3610 291810028 291809394 0.000000e+00 911
14 TraesCS1D01G352700 chr2B 92.622 637 38 5 2983 3610 754885198 754884562 0.000000e+00 907


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 TraesCS1D01G352700 chr1D 438256145 438259754 3609 True 6667.0 6667 100.000 1 3610 1 chr1D.!!$R1 3609
1 TraesCS1D01G352700 chr1D 478398180 478398817 637 True 948.0 948 93.730 2982 3610 1 chr1D.!!$R2 628
2 TraesCS1D01G352700 chr1A 534940778 534943668 2890 True 1603.5 2771 89.568 167 2973 2 chr1A.!!$R1 2806
3 TraesCS1D01G352700 chr1B 593888997 593891912 2915 True 1049.0 2723 90.975 166 2983 3 chr1B.!!$R1 2817
4 TraesCS1D01G352700 chr5B 243414012 243414648 636 True 963.0 963 94.192 2983 3610 1 chr5B.!!$R1 627
5 TraesCS1D01G352700 chr5B 282018562 282019195 633 True 909.0 909 92.767 2984 3610 1 chr5B.!!$R2 626
6 TraesCS1D01G352700 chr2D 446308472 446309109 637 False 953.0 953 93.887 2983 3610 1 chr2D.!!$F1 627
7 TraesCS1D01G352700 chr2D 619422543 619423182 639 False 937.0 937 93.292 2979 3610 1 chr2D.!!$F2 631
8 TraesCS1D01G352700 chr7B 746375558 746376199 641 True 917.0 917 92.679 2977 3608 1 chr7B.!!$R1 631
9 TraesCS1D01G352700 chr7B 606064794 606065428 634 False 900.0 900 92.441 2984 3610 1 chr7B.!!$F1 626
10 TraesCS1D01G352700 chr4B 291809394 291810028 634 True 911.0 911 92.756 2984 3610 1 chr4B.!!$R1 626
11 TraesCS1D01G352700 chr2B 754884562 754885198 636 True 907.0 907 92.622 2983 3610 1 chr2B.!!$R1 627

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
33 34 0.024238 CGCGAGTCGAAGATGCTTTG 59.976 55.0 18.61 0.00 40.67 2.77 F
448 478 0.028902 CGGTGCTGTCATGCATCATG 59.971 55.0 0.00 0.59 43.71 3.07 F
471 501 0.034337 ACCTAAACTCGAAAGCGCCA 59.966 50.0 2.29 0.00 37.46 5.69 F
1052 1158 0.313987 GCCAACAAGCCCAAGTGTAC 59.686 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1394 0.252197 GTAGCCCTGGGTCGATGTTT 59.748 55.000 15.56 0.00 0.00 2.83 R
1286 1403 1.281867 TGACAAAGATGTAGCCCTGGG 59.718 52.381 8.86 8.86 40.74 4.45 R
1679 1800 1.883638 GCCATGTTCTTCAGGACTGCA 60.884 52.381 0.00 0.00 0.00 4.41 R
2876 3148 0.454957 GCTCGTCGTAGCACCGTTAA 60.455 55.000 10.53 0.00 42.30 2.01 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
21 22 2.504244 CGGACAGAACCGCGAGTC 60.504 66.667 8.23 3.90 46.20 3.36
22 23 2.504244 GGACAGAACCGCGAGTCG 60.504 66.667 8.23 8.54 38.08 4.18
23 24 2.559840 GACAGAACCGCGAGTCGA 59.440 61.111 18.61 0.00 41.67 4.20
24 25 1.081641 GACAGAACCGCGAGTCGAA 60.082 57.895 18.61 0.00 41.67 3.71
25 26 1.066114 GACAGAACCGCGAGTCGAAG 61.066 60.000 18.61 8.79 41.67 3.79
26 27 1.209383 CAGAACCGCGAGTCGAAGA 59.791 57.895 18.61 0.00 41.67 2.87
27 28 0.179161 CAGAACCGCGAGTCGAAGAT 60.179 55.000 18.61 0.10 40.67 2.40
28 29 0.179161 AGAACCGCGAGTCGAAGATG 60.179 55.000 18.61 1.17 40.67 2.90
29 30 1.743855 GAACCGCGAGTCGAAGATGC 61.744 60.000 18.61 0.00 40.67 3.91
30 31 2.103143 CCGCGAGTCGAAGATGCT 59.897 61.111 18.61 0.00 40.67 3.79
31 32 1.517257 CCGCGAGTCGAAGATGCTT 60.517 57.895 18.61 0.00 40.67 3.91
32 33 1.078759 CCGCGAGTCGAAGATGCTTT 61.079 55.000 18.61 0.00 40.67 3.51
33 34 0.024238 CGCGAGTCGAAGATGCTTTG 59.976 55.000 18.61 0.00 40.67 2.77
34 35 0.371645 GCGAGTCGAAGATGCTTTGG 59.628 55.000 18.61 0.00 40.67 3.28
35 36 0.371645 CGAGTCGAAGATGCTTTGGC 59.628 55.000 6.73 0.00 40.67 4.52
52 53 2.818130 GGCAACAAGGATCTTGCAAA 57.182 45.000 16.47 0.00 43.89 3.68
53 54 3.110447 GGCAACAAGGATCTTGCAAAA 57.890 42.857 16.47 0.00 43.89 2.44
54 55 3.062042 GGCAACAAGGATCTTGCAAAAG 58.938 45.455 16.47 0.00 43.89 2.27
55 56 2.477754 GCAACAAGGATCTTGCAAAAGC 59.522 45.455 11.39 0.00 42.05 3.51
56 57 3.719924 CAACAAGGATCTTGCAAAAGCA 58.280 40.909 0.00 0.00 0.00 3.91
57 58 4.121317 CAACAAGGATCTTGCAAAAGCAA 58.879 39.130 0.00 2.69 0.00 3.91
58 59 3.721035 ACAAGGATCTTGCAAAAGCAAC 58.279 40.909 0.00 0.00 0.00 4.17
59 60 3.132646 ACAAGGATCTTGCAAAAGCAACA 59.867 39.130 0.00 0.00 0.00 3.33
60 61 4.121317 CAAGGATCTTGCAAAAGCAACAA 58.879 39.130 0.00 0.00 0.00 2.83
61 62 3.986277 AGGATCTTGCAAAAGCAACAAG 58.014 40.909 0.00 0.00 41.70 3.16
65 66 4.032703 TCTTGCAAAAGCAACAAGAGTC 57.967 40.909 0.00 0.00 43.55 3.36
66 67 3.696051 TCTTGCAAAAGCAACAAGAGTCT 59.304 39.130 0.00 0.00 43.55 3.24
67 68 4.158394 TCTTGCAAAAGCAACAAGAGTCTT 59.842 37.500 0.00 0.00 43.55 3.01
68 69 3.772932 TGCAAAAGCAACAAGAGTCTTG 58.227 40.909 27.66 27.66 0.00 3.02
69 70 3.193267 TGCAAAAGCAACAAGAGTCTTGT 59.807 39.130 28.97 28.97 0.00 3.16
70 71 4.176271 GCAAAAGCAACAAGAGTCTTGTT 58.824 39.130 35.15 35.15 42.75 2.83
77 78 3.266510 ACAAGAGTCTTGTTGCAGTGA 57.733 42.857 28.97 0.00 31.07 3.41
78 79 3.201290 ACAAGAGTCTTGTTGCAGTGAG 58.799 45.455 28.97 5.46 31.07 3.51
79 80 3.118629 ACAAGAGTCTTGTTGCAGTGAGA 60.119 43.478 28.97 0.00 31.07 3.27
80 81 3.383620 AGAGTCTTGTTGCAGTGAGAG 57.616 47.619 0.00 0.00 0.00 3.20
81 82 2.961741 AGAGTCTTGTTGCAGTGAGAGA 59.038 45.455 0.00 0.00 0.00 3.10
82 83 3.386078 AGAGTCTTGTTGCAGTGAGAGAA 59.614 43.478 0.00 0.00 0.00 2.87
83 84 4.122776 GAGTCTTGTTGCAGTGAGAGAAA 58.877 43.478 0.00 0.00 0.00 2.52
84 85 4.712476 AGTCTTGTTGCAGTGAGAGAAAT 58.288 39.130 0.00 0.00 0.00 2.17
85 86 5.858381 AGTCTTGTTGCAGTGAGAGAAATA 58.142 37.500 0.00 0.00 0.00 1.40
86 87 5.931146 AGTCTTGTTGCAGTGAGAGAAATAG 59.069 40.000 0.00 0.00 0.00 1.73
87 88 5.121454 GTCTTGTTGCAGTGAGAGAAATAGG 59.879 44.000 0.00 0.00 0.00 2.57
88 89 3.942829 TGTTGCAGTGAGAGAAATAGGG 58.057 45.455 0.00 0.00 0.00 3.53
89 90 3.582647 TGTTGCAGTGAGAGAAATAGGGA 59.417 43.478 0.00 0.00 0.00 4.20
90 91 4.041567 TGTTGCAGTGAGAGAAATAGGGAA 59.958 41.667 0.00 0.00 0.00 3.97
91 92 4.478206 TGCAGTGAGAGAAATAGGGAAG 57.522 45.455 0.00 0.00 0.00 3.46
92 93 4.096681 TGCAGTGAGAGAAATAGGGAAGA 58.903 43.478 0.00 0.00 0.00 2.87
93 94 4.161189 TGCAGTGAGAGAAATAGGGAAGAG 59.839 45.833 0.00 0.00 0.00 2.85
94 95 4.442753 GCAGTGAGAGAAATAGGGAAGAGG 60.443 50.000 0.00 0.00 0.00 3.69
95 96 4.959210 CAGTGAGAGAAATAGGGAAGAGGA 59.041 45.833 0.00 0.00 0.00 3.71
96 97 5.423610 CAGTGAGAGAAATAGGGAAGAGGAA 59.576 44.000 0.00 0.00 0.00 3.36
97 98 5.423931 AGTGAGAGAAATAGGGAAGAGGAAC 59.576 44.000 0.00 0.00 0.00 3.62
98 99 5.187967 GTGAGAGAAATAGGGAAGAGGAACA 59.812 44.000 0.00 0.00 0.00 3.18
99 100 5.187967 TGAGAGAAATAGGGAAGAGGAACAC 59.812 44.000 0.00 0.00 0.00 3.32
100 101 4.160626 AGAGAAATAGGGAAGAGGAACACG 59.839 45.833 0.00 0.00 0.00 4.49
101 102 4.094476 AGAAATAGGGAAGAGGAACACGA 58.906 43.478 0.00 0.00 0.00 4.35
102 103 4.530946 AGAAATAGGGAAGAGGAACACGAA 59.469 41.667 0.00 0.00 0.00 3.85
103 104 3.889520 ATAGGGAAGAGGAACACGAAC 57.110 47.619 0.00 0.00 0.00 3.95
104 105 1.420430 AGGGAAGAGGAACACGAACA 58.580 50.000 0.00 0.00 0.00 3.18
105 106 1.978580 AGGGAAGAGGAACACGAACAT 59.021 47.619 0.00 0.00 0.00 2.71
106 107 2.028020 AGGGAAGAGGAACACGAACATC 60.028 50.000 0.00 0.00 0.00 3.06
107 108 2.289444 GGGAAGAGGAACACGAACATCA 60.289 50.000 0.00 0.00 0.00 3.07
108 109 3.600388 GGAAGAGGAACACGAACATCAT 58.400 45.455 0.00 0.00 0.00 2.45
109 110 4.382685 GGGAAGAGGAACACGAACATCATA 60.383 45.833 0.00 0.00 0.00 2.15
110 111 4.567159 GGAAGAGGAACACGAACATCATAC 59.433 45.833 0.00 0.00 0.00 2.39
111 112 3.770666 AGAGGAACACGAACATCATACG 58.229 45.455 0.00 0.00 0.00 3.06
112 113 2.858344 GAGGAACACGAACATCATACGG 59.142 50.000 0.00 0.00 0.00 4.02
113 114 2.232941 AGGAACACGAACATCATACGGT 59.767 45.455 0.00 0.00 0.00 4.83
114 115 2.601763 GGAACACGAACATCATACGGTC 59.398 50.000 0.00 0.00 0.00 4.79
115 116 1.904144 ACACGAACATCATACGGTCG 58.096 50.000 0.00 0.00 0.00 4.79
116 117 1.469703 ACACGAACATCATACGGTCGA 59.530 47.619 4.41 0.00 0.00 4.20
117 118 2.109463 CACGAACATCATACGGTCGAG 58.891 52.381 4.41 0.00 0.00 4.04
118 119 1.121240 CGAACATCATACGGTCGAGC 58.879 55.000 4.06 4.06 0.00 5.03
119 120 1.121240 GAACATCATACGGTCGAGCG 58.879 55.000 33.08 33.08 0.00 5.03
120 121 0.248907 AACATCATACGGTCGAGCGG 60.249 55.000 36.44 21.38 0.00 5.52
121 122 1.359117 CATCATACGGTCGAGCGGT 59.641 57.895 36.44 24.71 34.85 5.68
122 123 0.248907 CATCATACGGTCGAGCGGTT 60.249 55.000 36.44 22.46 32.68 4.44
123 124 0.030369 ATCATACGGTCGAGCGGTTC 59.970 55.000 36.44 0.34 32.68 3.62
148 149 2.511600 CCGACGGGCCAAGCTTAG 60.512 66.667 5.81 0.00 0.00 2.18
149 150 3.195698 CGACGGGCCAAGCTTAGC 61.196 66.667 8.50 8.50 0.00 3.09
150 151 2.046314 GACGGGCCAAGCTTAGCA 60.046 61.111 18.62 0.00 0.00 3.49
151 152 2.359975 ACGGGCCAAGCTTAGCAC 60.360 61.111 18.62 14.27 0.00 4.40
153 154 3.815396 GGGCCAAGCTTAGCACGC 61.815 66.667 18.62 4.27 0.00 5.34
154 155 2.747855 GGCCAAGCTTAGCACGCT 60.748 61.111 18.62 0.00 39.94 5.07
155 156 2.754995 GGCCAAGCTTAGCACGCTC 61.755 63.158 18.62 0.00 36.56 5.03
156 157 2.754995 GCCAAGCTTAGCACGCTCC 61.755 63.158 12.24 0.00 36.56 4.70
157 158 1.078848 CCAAGCTTAGCACGCTCCT 60.079 57.895 7.07 0.00 36.56 3.69
158 159 1.086634 CCAAGCTTAGCACGCTCCTC 61.087 60.000 7.07 0.00 36.56 3.71
159 160 0.390340 CAAGCTTAGCACGCTCCTCA 60.390 55.000 7.07 0.00 36.56 3.86
160 161 0.321671 AAGCTTAGCACGCTCCTCAA 59.678 50.000 7.07 0.00 36.56 3.02
161 162 0.321671 AGCTTAGCACGCTCCTCAAA 59.678 50.000 7.07 0.00 30.49 2.69
162 163 1.156736 GCTTAGCACGCTCCTCAAAA 58.843 50.000 0.00 0.00 0.00 2.44
163 164 1.535462 GCTTAGCACGCTCCTCAAAAA 59.465 47.619 0.00 0.00 0.00 1.94
187 188 0.821301 TGTTGCAAATCAGGGCGTGA 60.821 50.000 12.80 12.80 40.38 4.35
196 197 4.871933 AATCAGGGCGTGAAAAATCTTT 57.128 36.364 14.47 0.00 39.19 2.52
204 206 5.163804 GGGCGTGAAAAATCTTTGTTTGTTT 60.164 36.000 0.00 0.00 0.00 2.83
206 208 6.401581 GGCGTGAAAAATCTTTGTTTGTTTGA 60.402 34.615 0.00 0.00 0.00 2.69
219 221 6.279513 TGTTTGTTTGATTCTGAACCTTGT 57.720 33.333 0.00 0.00 0.00 3.16
228 230 2.683968 TCTGAACCTTGTCGTATGCAC 58.316 47.619 0.00 0.00 0.00 4.57
229 231 1.732259 CTGAACCTTGTCGTATGCACC 59.268 52.381 0.00 0.00 0.00 5.01
230 232 1.070914 TGAACCTTGTCGTATGCACCA 59.929 47.619 0.00 0.00 0.00 4.17
231 233 2.290008 TGAACCTTGTCGTATGCACCAT 60.290 45.455 0.00 0.00 0.00 3.55
233 235 1.555075 ACCTTGTCGTATGCACCATCT 59.445 47.619 0.00 0.00 0.00 2.90
245 257 1.004560 ACCATCTGCACCACTGTCG 60.005 57.895 0.00 0.00 0.00 4.35
271 283 2.701780 GCGAACGGCTCTCCTGAGA 61.702 63.158 0.00 0.00 42.73 3.27
283 295 3.125573 CTGAGACGCCGGAGTCGA 61.126 66.667 29.13 19.83 45.26 4.20
304 319 2.421739 GCAGTGGGGCGTCGATAT 59.578 61.111 0.00 0.00 0.00 1.63
306 321 0.666577 GCAGTGGGGCGTCGATATAC 60.667 60.000 0.00 0.00 0.00 1.47
307 322 0.386858 CAGTGGGGCGTCGATATACG 60.387 60.000 0.00 0.00 45.58 3.06
318 333 3.580794 TCGATATACGACACAGACACG 57.419 47.619 0.00 0.00 46.45 4.49
319 334 2.286025 TCGATATACGACACAGACACGG 59.714 50.000 0.00 0.00 46.45 4.94
320 335 2.382519 GATATACGACACAGACACGGC 58.617 52.381 0.00 0.00 0.00 5.68
321 336 0.452987 TATACGACACAGACACGGCC 59.547 55.000 0.00 0.00 0.00 6.13
322 337 1.529152 ATACGACACAGACACGGCCA 61.529 55.000 2.24 0.00 0.00 5.36
323 338 2.137425 TACGACACAGACACGGCCAG 62.137 60.000 2.24 0.00 0.00 4.85
324 339 2.357517 GACACAGACACGGCCAGG 60.358 66.667 2.24 0.00 0.00 4.45
325 340 4.626081 ACACAGACACGGCCAGGC 62.626 66.667 1.26 1.26 0.00 4.85
343 358 3.224324 CATCGATCCCCGTCCGGT 61.224 66.667 0.00 0.00 39.75 5.28
344 359 2.910994 ATCGATCCCCGTCCGGTC 60.911 66.667 0.00 0.00 39.75 4.79
400 425 4.986531 CGTGCGCGTGTTGGAACG 62.987 66.667 12.43 0.00 46.30 3.95
401 426 3.932313 GTGCGCGTGTTGGAACGT 61.932 61.111 8.43 0.00 45.32 3.99
402 427 3.632107 TGCGCGTGTTGGAACGTC 61.632 61.111 8.43 0.00 45.32 4.34
403 428 3.632107 GCGCGTGTTGGAACGTCA 61.632 61.111 8.43 0.00 45.32 4.35
407 436 0.315869 GCGTGTTGGAACGTCAGTTG 60.316 55.000 0.00 0.00 45.32 3.16
410 439 2.604011 CGTGTTGGAACGTCAGTTGTTA 59.396 45.455 0.00 0.00 41.34 2.41
448 478 0.028902 CGGTGCTGTCATGCATCATG 59.971 55.000 0.00 0.59 43.71 3.07
449 479 0.248907 GGTGCTGTCATGCATCATGC 60.249 55.000 1.35 1.35 45.23 4.06
461 491 3.959573 GCATCATGCAGACCTAAACTC 57.040 47.619 4.20 0.00 44.26 3.01
462 492 2.286294 GCATCATGCAGACCTAAACTCG 59.714 50.000 4.20 0.00 44.26 4.18
463 493 3.785486 CATCATGCAGACCTAAACTCGA 58.215 45.455 0.00 0.00 0.00 4.04
464 494 3.953712 TCATGCAGACCTAAACTCGAA 57.046 42.857 0.00 0.00 0.00 3.71
465 495 4.265904 TCATGCAGACCTAAACTCGAAA 57.734 40.909 0.00 0.00 0.00 3.46
470 500 0.720027 GACCTAAACTCGAAAGCGCC 59.280 55.000 2.29 0.00 37.46 6.53
471 501 0.034337 ACCTAAACTCGAAAGCGCCA 59.966 50.000 2.29 0.00 37.46 5.69
472 502 0.442699 CCTAAACTCGAAAGCGCCAC 59.557 55.000 2.29 0.00 37.46 5.01
473 503 1.144969 CTAAACTCGAAAGCGCCACA 58.855 50.000 2.29 0.00 37.46 4.17
474 504 0.863144 TAAACTCGAAAGCGCCACAC 59.137 50.000 2.29 0.00 37.46 3.82
475 505 1.092921 AAACTCGAAAGCGCCACACA 61.093 50.000 2.29 0.00 37.46 3.72
476 506 1.498865 AACTCGAAAGCGCCACACAG 61.499 55.000 2.29 0.00 37.46 3.66
477 507 3.300667 CTCGAAAGCGCCACACAGC 62.301 63.158 2.29 0.00 37.46 4.40
526 567 2.346099 GCACGAGGCAAAAATAGCAA 57.654 45.000 0.00 0.00 43.97 3.91
534 575 0.984109 CAAAAATAGCAACCGCGCAG 59.016 50.000 8.75 0.00 45.49 5.18
570 618 2.103736 GGCCCTGTACGTAGACGC 59.896 66.667 1.14 0.00 44.43 5.19
675 756 1.553308 GATGCGTACGAGGTAACCAC 58.447 55.000 21.65 0.00 37.17 4.16
794 884 1.944676 GCGATCACGATCACGACCC 60.945 63.158 7.75 0.00 42.66 4.46
796 886 1.299165 GATCACGATCACGACCCCG 60.299 63.158 2.09 0.00 42.66 5.73
797 887 1.721664 GATCACGATCACGACCCCGA 61.722 60.000 2.09 0.00 42.66 5.14
798 888 1.317431 ATCACGATCACGACCCCGAA 61.317 55.000 0.00 0.00 42.66 4.30
800 890 2.270257 ACGATCACGACCCCGAACA 61.270 57.895 0.00 0.00 42.66 3.18
802 892 1.804326 GATCACGACCCCGAACACG 60.804 63.158 0.00 0.00 39.50 4.49
803 893 2.203972 GATCACGACCCCGAACACGA 62.204 60.000 0.00 0.00 39.50 4.35
804 894 1.601419 ATCACGACCCCGAACACGAT 61.601 55.000 0.00 0.00 39.50 3.73
805 895 1.804326 CACGACCCCGAACACGATC 60.804 63.158 0.00 0.00 39.50 3.69
806 896 2.578713 CGACCCCGAACACGATCG 60.579 66.667 14.88 14.88 42.37 3.69
807 897 2.884207 GACCCCGAACACGATCGC 60.884 66.667 16.60 0.00 41.40 4.58
808 898 3.636313 GACCCCGAACACGATCGCA 62.636 63.158 16.60 0.00 41.40 5.10
809 899 2.885644 CCCCGAACACGATCGCAG 60.886 66.667 16.60 10.96 41.40 5.18
810 900 3.554692 CCCGAACACGATCGCAGC 61.555 66.667 16.60 1.23 41.40 5.25
811 901 3.554692 CCGAACACGATCGCAGCC 61.555 66.667 16.60 1.44 41.40 4.85
812 902 3.554692 CGAACACGATCGCAGCCC 61.555 66.667 16.60 2.98 35.85 5.19
813 903 3.195698 GAACACGATCGCAGCCCC 61.196 66.667 16.60 0.00 0.00 5.80
859 949 1.001048 CCGCCGTCGATCAGGTAATTA 60.001 52.381 0.00 0.00 38.10 1.40
860 950 2.544277 CCGCCGTCGATCAGGTAATTAA 60.544 50.000 0.00 0.00 38.10 1.40
861 951 3.314553 CGCCGTCGATCAGGTAATTAAT 58.685 45.455 0.00 0.00 38.10 1.40
862 952 3.739300 CGCCGTCGATCAGGTAATTAATT 59.261 43.478 5.89 5.89 38.10 1.40
886 983 5.435041 TGGTTTGGTATATGATCCCCTTCTT 59.565 40.000 0.00 0.00 0.00 2.52
913 1010 2.280389 CCGATCAGGGACGGCATG 60.280 66.667 0.00 0.00 42.55 4.06
927 1024 1.164411 GGCATGAACGTGTGATTCCA 58.836 50.000 0.00 0.00 0.00 3.53
989 1086 1.265635 TGGTTGATTTTCTTCCGTGCG 59.734 47.619 0.00 0.00 0.00 5.34
1052 1158 0.313987 GCCAACAAGCCCAAGTGTAC 59.686 55.000 0.00 0.00 0.00 2.90
1068 1182 1.447140 TACGTCTGATTGTGCCGCC 60.447 57.895 0.00 0.00 0.00 6.13
1266 1383 6.471976 TTGTTTCTTCTCTTGTGATGATCG 57.528 37.500 0.00 0.00 0.00 3.69
1277 1394 5.411053 TCTTGTGATGATCGTTGCAAATGTA 59.589 36.000 0.00 0.00 33.60 2.29
1286 1403 4.459606 TCGTTGCAAATGTAAACATCGAC 58.540 39.130 0.00 0.00 35.10 4.20
1318 1435 6.560253 ACATCTTTGTCAACCTGAATGTAC 57.440 37.500 0.00 0.00 0.00 2.90
1331 1448 7.200434 ACCTGAATGTACTAACATGAATCCT 57.800 36.000 0.00 0.00 45.79 3.24
1499 1620 1.173043 TGCTGTTCCCTAATTTGCCG 58.827 50.000 0.00 0.00 0.00 5.69
1503 1624 2.354821 CTGTTCCCTAATTTGCCGCTAC 59.645 50.000 0.00 0.00 0.00 3.58
1585 1706 2.168521 GACAAGATCGGGTTCATCCAGA 59.831 50.000 0.00 0.00 43.89 3.86
1665 1786 4.867047 TCTTCTCATTCAGAAATGCGTCTC 59.133 41.667 0.00 0.00 40.83 3.36
1666 1787 4.462508 TCTCATTCAGAAATGCGTCTCT 57.537 40.909 0.00 0.00 41.76 3.10
1670 1791 5.344066 TCATTCAGAAATGCGTCTCTACTC 58.656 41.667 0.00 0.00 41.76 2.59
1678 1799 1.339727 TGCGTCTCTACTCTGCTGGTA 60.340 52.381 0.00 0.00 0.00 3.25
1679 1800 1.950909 GCGTCTCTACTCTGCTGGTAT 59.049 52.381 0.00 0.00 0.00 2.73
2097 2230 2.329379 CTCAACGACAAGCTACCTGTC 58.671 52.381 6.92 6.92 0.00 3.51
2104 2237 2.297597 GACAAGCTACCTGTCTGTGACT 59.702 50.000 9.35 0.00 33.15 3.41
2105 2238 3.497332 ACAAGCTACCTGTCTGTGACTA 58.503 45.455 0.00 0.00 33.15 2.59
2106 2239 3.895656 ACAAGCTACCTGTCTGTGACTAA 59.104 43.478 0.00 0.00 33.15 2.24
2107 2240 4.528596 ACAAGCTACCTGTCTGTGACTAAT 59.471 41.667 0.00 0.00 33.15 1.73
2108 2241 5.012148 ACAAGCTACCTGTCTGTGACTAATT 59.988 40.000 0.00 0.00 33.15 1.40
2116 2249 5.120830 CCTGTCTGTGACTAATTAAGTGCAC 59.879 44.000 9.40 9.40 39.07 4.57
2117 2250 5.606505 TGTCTGTGACTAATTAAGTGCACA 58.393 37.500 21.04 0.00 40.65 4.57
2118 2251 6.052360 TGTCTGTGACTAATTAAGTGCACAA 58.948 36.000 21.04 5.76 41.47 3.33
2122 2255 7.497579 TCTGTGACTAATTAAGTGCACAAAGAA 59.502 33.333 21.04 7.39 41.47 2.52
2123 2256 8.165239 TGTGACTAATTAAGTGCACAAAGAAT 57.835 30.769 21.04 9.43 40.31 2.40
2132 2265 9.683069 ATTAAGTGCACAAAGAATTAACTTCTG 57.317 29.630 21.04 0.00 43.60 3.02
2136 2269 6.638468 GTGCACAAAGAATTAACTTCTGAAGG 59.362 38.462 20.61 4.16 43.60 3.46
2137 2270 6.545666 TGCACAAAGAATTAACTTCTGAAGGA 59.454 34.615 20.61 6.30 43.60 3.36
2141 2274 9.225436 ACAAAGAATTAACTTCTGAAGGATCTC 57.775 33.333 20.61 10.43 43.60 2.75
2149 2282 4.141892 ACTTCTGAAGGATCTCTGATGCAG 60.142 45.833 20.61 0.00 0.00 4.41
2471 2635 3.373130 GTCGTCAAGCCAAGGTAAATACC 59.627 47.826 1.16 1.16 46.82 2.73
2485 2649 4.516698 GGTAAATACCAGCATCTGACATGG 59.483 45.833 4.72 3.74 45.73 3.66
2509 2691 7.068962 TGGTTATGTGCAGATCATTCATTCATT 59.931 33.333 0.00 0.00 0.00 2.57
2625 2807 1.394917 ACTGAATGCGACGCTGAAATC 59.605 47.619 22.08 11.79 0.00 2.17
2644 2826 0.596082 CACAAGGCCCGTTTTGTAGG 59.404 55.000 7.70 0.00 35.86 3.18
2652 2834 0.446222 CCGTTTTGTAGGTGGATGCG 59.554 55.000 0.00 0.00 0.00 4.73
2683 2949 4.386230 CGTCTCAAACGTTGCTTTCTATG 58.614 43.478 0.00 0.00 46.42 2.23
2699 2965 2.367894 TCTATGCCTTCCTGAGCATCTG 59.632 50.000 0.00 0.00 46.58 2.90
2700 2966 1.210538 ATGCCTTCCTGAGCATCTGA 58.789 50.000 0.00 0.00 46.58 3.27
2820 3092 3.466836 TGTTTCCTGTTCAGTAGCTGTG 58.533 45.455 0.00 0.00 32.61 3.66
2911 3183 2.744709 GCTTACGCCGGCCTGAAA 60.745 61.111 23.46 9.03 0.00 2.69
2929 3201 6.183360 GCCTGAAACTTTGCATTAATAAACCG 60.183 38.462 0.00 0.00 0.00 4.44
2944 3216 9.895138 ATTAATAAACCGGAGTACATTTACAGT 57.105 29.630 9.46 0.00 0.00 3.55
3106 3387 1.331756 GCCACCATCTAAGCAACATCG 59.668 52.381 0.00 0.00 0.00 3.84
3141 3422 0.107703 CAGTTGATGAAGGGGCGCTA 60.108 55.000 7.64 0.00 0.00 4.26
3184 3465 2.032681 ACCTCGCAGCCAAACCTC 59.967 61.111 0.00 0.00 0.00 3.85
3406 3687 3.362399 CTCCTGCGCGTGTCCATCT 62.362 63.158 8.43 0.00 0.00 2.90
3421 3702 1.205655 CCATCTCCACACATCTGACGT 59.794 52.381 0.00 0.00 0.00 4.34
3422 3703 2.265683 CATCTCCACACATCTGACGTG 58.734 52.381 1.83 1.83 40.32 4.49
3542 3824 1.005097 AGTGCATCTCCAAGAATGCCA 59.995 47.619 5.01 0.00 39.12 4.92
3548 3831 1.856873 TCCAAGAATGCCACCCCCT 60.857 57.895 0.00 0.00 0.00 4.79
3592 3875 1.154205 GCCGTCATCCGATCAACTGG 61.154 60.000 0.00 0.00 39.56 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.467946 TTCGACTCGCGGTTCTGTCC 62.468 60.000 6.13 0.00 41.33 4.02
6 7 1.066114 CTTCGACTCGCGGTTCTGTC 61.066 60.000 6.13 6.66 41.33 3.51
7 8 1.081376 CTTCGACTCGCGGTTCTGT 60.081 57.895 6.13 0.00 41.33 3.41
8 9 0.179161 ATCTTCGACTCGCGGTTCTG 60.179 55.000 6.13 0.18 41.33 3.02
9 10 0.179161 CATCTTCGACTCGCGGTTCT 60.179 55.000 6.13 0.00 41.33 3.01
10 11 1.743855 GCATCTTCGACTCGCGGTTC 61.744 60.000 6.13 1.46 41.33 3.62
11 12 1.805945 GCATCTTCGACTCGCGGTT 60.806 57.895 6.13 0.00 41.33 4.44
12 13 2.202623 GCATCTTCGACTCGCGGT 60.203 61.111 6.13 2.39 41.33 5.68
13 14 1.078759 AAAGCATCTTCGACTCGCGG 61.079 55.000 6.13 0.00 41.33 6.46
14 15 0.024238 CAAAGCATCTTCGACTCGCG 59.976 55.000 0.00 0.00 42.69 5.87
15 16 0.371645 CCAAAGCATCTTCGACTCGC 59.628 55.000 0.00 0.00 0.00 5.03
16 17 0.371645 GCCAAAGCATCTTCGACTCG 59.628 55.000 0.00 0.00 39.53 4.18
17 18 1.442769 TGCCAAAGCATCTTCGACTC 58.557 50.000 0.00 0.00 46.52 3.36
18 19 3.631453 TGCCAAAGCATCTTCGACT 57.369 47.368 0.00 0.00 46.52 4.18
28 29 2.680577 CAAGATCCTTGTTGCCAAAGC 58.319 47.619 0.00 0.00 40.48 3.51
29 30 2.680577 GCAAGATCCTTGTTGCCAAAG 58.319 47.619 6.20 0.00 44.19 2.77
30 31 2.818130 GCAAGATCCTTGTTGCCAAA 57.182 45.000 6.20 0.00 44.19 3.28
56 57 3.609853 TCACTGCAACAAGACTCTTGTT 58.390 40.909 25.39 25.39 42.75 2.83
57 58 3.118629 TCTCACTGCAACAAGACTCTTGT 60.119 43.478 17.29 17.29 0.00 3.16
58 59 3.461061 TCTCACTGCAACAAGACTCTTG 58.539 45.455 16.01 16.01 0.00 3.02
59 60 3.386078 TCTCTCACTGCAACAAGACTCTT 59.614 43.478 0.00 0.00 0.00 2.85
60 61 2.961741 TCTCTCACTGCAACAAGACTCT 59.038 45.455 0.00 0.00 0.00 3.24
61 62 3.377346 TCTCTCACTGCAACAAGACTC 57.623 47.619 0.00 0.00 0.00 3.36
62 63 3.827008 TTCTCTCACTGCAACAAGACT 57.173 42.857 0.00 0.00 0.00 3.24
63 64 5.121454 CCTATTTCTCTCACTGCAACAAGAC 59.879 44.000 0.00 0.00 0.00 3.01
64 65 5.240891 CCTATTTCTCTCACTGCAACAAGA 58.759 41.667 0.00 0.00 0.00 3.02
65 66 4.394300 CCCTATTTCTCTCACTGCAACAAG 59.606 45.833 0.00 0.00 0.00 3.16
66 67 4.041567 TCCCTATTTCTCTCACTGCAACAA 59.958 41.667 0.00 0.00 0.00 2.83
67 68 3.582647 TCCCTATTTCTCTCACTGCAACA 59.417 43.478 0.00 0.00 0.00 3.33
68 69 4.207891 TCCCTATTTCTCTCACTGCAAC 57.792 45.455 0.00 0.00 0.00 4.17
69 70 4.532126 TCTTCCCTATTTCTCTCACTGCAA 59.468 41.667 0.00 0.00 0.00 4.08
70 71 4.096681 TCTTCCCTATTTCTCTCACTGCA 58.903 43.478 0.00 0.00 0.00 4.41
71 72 4.442753 CCTCTTCCCTATTTCTCTCACTGC 60.443 50.000 0.00 0.00 0.00 4.40
72 73 4.959210 TCCTCTTCCCTATTTCTCTCACTG 59.041 45.833 0.00 0.00 0.00 3.66
73 74 5.213868 TCCTCTTCCCTATTTCTCTCACT 57.786 43.478 0.00 0.00 0.00 3.41
74 75 5.187967 TGTTCCTCTTCCCTATTTCTCTCAC 59.812 44.000 0.00 0.00 0.00 3.51
75 76 5.187967 GTGTTCCTCTTCCCTATTTCTCTCA 59.812 44.000 0.00 0.00 0.00 3.27
76 77 5.666462 GTGTTCCTCTTCCCTATTTCTCTC 58.334 45.833 0.00 0.00 0.00 3.20
77 78 4.160626 CGTGTTCCTCTTCCCTATTTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
78 79 4.159879 TCGTGTTCCTCTTCCCTATTTCTC 59.840 45.833 0.00 0.00 0.00 2.87
79 80 4.094476 TCGTGTTCCTCTTCCCTATTTCT 58.906 43.478 0.00 0.00 0.00 2.52
80 81 4.467198 TCGTGTTCCTCTTCCCTATTTC 57.533 45.455 0.00 0.00 0.00 2.17
81 82 4.041198 TGTTCGTGTTCCTCTTCCCTATTT 59.959 41.667 0.00 0.00 0.00 1.40
82 83 3.581332 TGTTCGTGTTCCTCTTCCCTATT 59.419 43.478 0.00 0.00 0.00 1.73
83 84 3.170717 TGTTCGTGTTCCTCTTCCCTAT 58.829 45.455 0.00 0.00 0.00 2.57
84 85 2.600790 TGTTCGTGTTCCTCTTCCCTA 58.399 47.619 0.00 0.00 0.00 3.53
85 86 1.420430 TGTTCGTGTTCCTCTTCCCT 58.580 50.000 0.00 0.00 0.00 4.20
86 87 2.289444 TGATGTTCGTGTTCCTCTTCCC 60.289 50.000 0.00 0.00 0.00 3.97
87 88 3.040147 TGATGTTCGTGTTCCTCTTCC 57.960 47.619 0.00 0.00 0.00 3.46
88 89 4.265556 CGTATGATGTTCGTGTTCCTCTTC 59.734 45.833 0.00 0.00 0.00 2.87
89 90 4.174009 CGTATGATGTTCGTGTTCCTCTT 58.826 43.478 0.00 0.00 0.00 2.85
90 91 3.428999 CCGTATGATGTTCGTGTTCCTCT 60.429 47.826 0.00 0.00 0.00 3.69
91 92 2.858344 CCGTATGATGTTCGTGTTCCTC 59.142 50.000 0.00 0.00 0.00 3.71
92 93 2.232941 ACCGTATGATGTTCGTGTTCCT 59.767 45.455 0.00 0.00 0.00 3.36
93 94 2.601763 GACCGTATGATGTTCGTGTTCC 59.398 50.000 0.00 0.00 0.00 3.62
94 95 2.278094 CGACCGTATGATGTTCGTGTTC 59.722 50.000 0.00 0.00 0.00 3.18
95 96 2.095110 TCGACCGTATGATGTTCGTGTT 60.095 45.455 0.00 0.00 0.00 3.32
96 97 1.469703 TCGACCGTATGATGTTCGTGT 59.530 47.619 0.00 0.00 0.00 4.49
97 98 2.109463 CTCGACCGTATGATGTTCGTG 58.891 52.381 0.00 0.00 0.00 4.35
98 99 1.533338 GCTCGACCGTATGATGTTCGT 60.533 52.381 0.00 0.00 0.00 3.85
99 100 1.121240 GCTCGACCGTATGATGTTCG 58.879 55.000 0.00 0.00 0.00 3.95
100 101 1.121240 CGCTCGACCGTATGATGTTC 58.879 55.000 0.00 0.00 0.00 3.18
101 102 0.248907 CCGCTCGACCGTATGATGTT 60.249 55.000 0.00 0.00 0.00 2.71
102 103 1.359117 CCGCTCGACCGTATGATGT 59.641 57.895 0.00 0.00 0.00 3.06
103 104 0.248907 AACCGCTCGACCGTATGATG 60.249 55.000 0.00 0.00 0.00 3.07
104 105 0.030369 GAACCGCTCGACCGTATGAT 59.970 55.000 0.00 0.00 0.00 2.45
105 106 1.430632 GAACCGCTCGACCGTATGA 59.569 57.895 0.00 0.00 0.00 2.15
106 107 3.993103 GAACCGCTCGACCGTATG 58.007 61.111 0.00 0.00 0.00 2.39
131 132 2.511600 CTAAGCTTGGCCCGTCGG 60.512 66.667 9.86 3.60 0.00 4.79
132 133 3.195698 GCTAAGCTTGGCCCGTCG 61.196 66.667 23.14 0.00 0.00 5.12
133 134 2.046314 TGCTAAGCTTGGCCCGTC 60.046 61.111 29.17 4.97 33.25 4.79
134 135 2.359975 GTGCTAAGCTTGGCCCGT 60.360 61.111 29.17 0.00 33.25 5.28
135 136 3.499737 CGTGCTAAGCTTGGCCCG 61.500 66.667 29.17 26.19 33.25 6.13
136 137 3.815396 GCGTGCTAAGCTTGGCCC 61.815 66.667 29.17 18.96 33.25 5.80
137 138 2.747855 AGCGTGCTAAGCTTGGCC 60.748 61.111 29.17 19.62 43.24 5.36
138 139 2.754995 GGAGCGTGCTAAGCTTGGC 61.755 63.158 26.32 26.32 46.13 4.52
139 140 1.078848 AGGAGCGTGCTAAGCTTGG 60.079 57.895 9.86 7.48 46.13 3.61
140 141 0.390340 TGAGGAGCGTGCTAAGCTTG 60.390 55.000 9.86 0.01 46.13 4.01
141 142 0.321671 TTGAGGAGCGTGCTAAGCTT 59.678 50.000 3.48 3.48 46.13 3.74
143 144 1.156736 TTTTGAGGAGCGTGCTAAGC 58.843 50.000 0.00 0.00 0.00 3.09
161 162 3.565063 GCCCTGATTTGCAACATGTTTTT 59.435 39.130 8.77 0.00 0.00 1.94
162 163 3.140623 GCCCTGATTTGCAACATGTTTT 58.859 40.909 8.77 0.00 0.00 2.43
163 164 2.769893 GCCCTGATTTGCAACATGTTT 58.230 42.857 8.77 0.00 0.00 2.83
164 165 1.337074 CGCCCTGATTTGCAACATGTT 60.337 47.619 4.92 4.92 0.00 2.71
179 180 4.119136 CAAACAAAGATTTTTCACGCCCT 58.881 39.130 0.00 0.00 0.00 5.19
180 181 3.868661 ACAAACAAAGATTTTTCACGCCC 59.131 39.130 0.00 0.00 0.00 6.13
181 182 5.463499 AACAAACAAAGATTTTTCACGCC 57.537 34.783 0.00 0.00 0.00 5.68
196 197 6.279513 ACAAGGTTCAGAATCAAACAAACA 57.720 33.333 0.00 0.00 0.00 2.83
204 206 3.932710 GCATACGACAAGGTTCAGAATCA 59.067 43.478 0.00 0.00 0.00 2.57
206 208 3.684788 GTGCATACGACAAGGTTCAGAAT 59.315 43.478 0.00 0.00 0.00 2.40
228 230 1.742880 CCGACAGTGGTGCAGATGG 60.743 63.158 0.00 0.00 0.00 3.51
229 231 0.603707 AACCGACAGTGGTGCAGATG 60.604 55.000 0.00 0.00 42.89 2.90
230 232 0.108585 AAACCGACAGTGGTGCAGAT 59.891 50.000 0.00 0.00 42.89 2.90
231 233 0.813610 CAAACCGACAGTGGTGCAGA 60.814 55.000 0.00 0.00 42.89 4.26
233 235 2.477176 GCAAACCGACAGTGGTGCA 61.477 57.895 0.00 0.00 42.89 4.57
236 248 2.590575 CCGCAAACCGACAGTGGT 60.591 61.111 0.00 0.00 46.67 4.16
241 253 3.641986 GTTCGCCGCAAACCGACA 61.642 61.111 0.00 0.00 40.02 4.35
267 279 2.670592 TTCGACTCCGGCGTCTCA 60.671 61.111 21.54 6.04 36.24 3.27
289 301 0.535780 TCGTATATCGACGCCCCACT 60.536 55.000 0.00 0.00 44.01 4.00
300 312 2.382519 GCCGTGTCTGTGTCGTATATC 58.617 52.381 0.00 0.00 0.00 1.63
304 319 2.137425 CTGGCCGTGTCTGTGTCGTA 62.137 60.000 0.00 0.00 0.00 3.43
306 321 2.734723 CTGGCCGTGTCTGTGTCG 60.735 66.667 0.00 0.00 0.00 4.35
307 322 2.357517 CCTGGCCGTGTCTGTGTC 60.358 66.667 0.00 0.00 0.00 3.67
308 323 4.626081 GCCTGGCCGTGTCTGTGT 62.626 66.667 7.66 0.00 0.00 3.72
319 334 4.650377 GGGGATCGATGGCCTGGC 62.650 72.222 11.05 11.05 0.00 4.85
320 335 4.320456 CGGGGATCGATGGCCTGG 62.320 72.222 0.54 0.00 42.43 4.45
321 336 3.521529 GACGGGGATCGATGGCCTG 62.522 68.421 0.54 0.00 42.43 4.85
322 337 3.234730 GACGGGGATCGATGGCCT 61.235 66.667 0.54 0.00 42.43 5.19
323 338 4.315941 GGACGGGGATCGATGGCC 62.316 72.222 0.54 0.00 42.43 5.36
324 339 4.664677 CGGACGGGGATCGATGGC 62.665 72.222 0.54 0.00 42.43 4.40
325 340 3.991051 CCGGACGGGGATCGATGG 61.991 72.222 0.54 0.00 42.43 3.51
326 341 3.208884 GACCGGACGGGGATCGATG 62.209 68.421 9.46 0.00 42.43 3.84
327 342 2.910994 GACCGGACGGGGATCGAT 60.911 66.667 9.46 0.00 42.43 3.59
394 419 4.951254 TCTGAATAACAACTGACGTTCCA 58.049 39.130 0.00 0.00 0.00 3.53
396 421 4.433022 CGCTCTGAATAACAACTGACGTTC 60.433 45.833 0.00 0.00 0.00 3.95
400 425 3.059570 CGACGCTCTGAATAACAACTGAC 59.940 47.826 0.00 0.00 0.00 3.51
401 426 3.242518 CGACGCTCTGAATAACAACTGA 58.757 45.455 0.00 0.00 0.00 3.41
402 427 2.222596 GCGACGCTCTGAATAACAACTG 60.223 50.000 13.73 0.00 0.00 3.16
403 428 1.993370 GCGACGCTCTGAATAACAACT 59.007 47.619 13.73 0.00 0.00 3.16
448 478 1.390463 CGCTTTCGAGTTTAGGTCTGC 59.610 52.381 0.00 0.00 38.10 4.26
449 479 1.390463 GCGCTTTCGAGTTTAGGTCTG 59.610 52.381 0.00 0.00 38.10 3.51
450 480 1.672145 GGCGCTTTCGAGTTTAGGTCT 60.672 52.381 7.64 0.00 38.10 3.85
452 482 0.034337 TGGCGCTTTCGAGTTTAGGT 59.966 50.000 7.64 0.00 38.10 3.08
453 483 0.442699 GTGGCGCTTTCGAGTTTAGG 59.557 55.000 7.64 0.00 38.10 2.69
454 484 1.136336 GTGTGGCGCTTTCGAGTTTAG 60.136 52.381 7.64 0.00 38.10 1.85
455 485 0.863144 GTGTGGCGCTTTCGAGTTTA 59.137 50.000 7.64 0.00 38.10 2.01
457 487 1.498865 CTGTGTGGCGCTTTCGAGTT 61.499 55.000 7.64 0.00 38.10 3.01
459 489 2.856032 CTGTGTGGCGCTTTCGAG 59.144 61.111 7.64 0.00 38.10 4.04
460 490 3.345808 GCTGTGTGGCGCTTTCGA 61.346 61.111 7.64 0.00 38.10 3.71
461 491 2.770587 GAAGCTGTGTGGCGCTTTCG 62.771 60.000 7.64 0.00 45.70 3.46
462 492 1.081840 GAAGCTGTGTGGCGCTTTC 60.082 57.895 7.64 0.00 45.70 2.62
463 493 2.896801 CGAAGCTGTGTGGCGCTTT 61.897 57.895 7.64 0.00 45.70 3.51
465 495 4.609018 ACGAAGCTGTGTGGCGCT 62.609 61.111 7.64 0.00 38.30 5.92
470 500 1.795286 GGAAAGAGACGAAGCTGTGTG 59.205 52.381 0.00 0.00 0.00 3.82
471 501 1.270358 GGGAAAGAGACGAAGCTGTGT 60.270 52.381 0.00 0.00 0.00 3.72
472 502 1.433534 GGGAAAGAGACGAAGCTGTG 58.566 55.000 0.00 0.00 0.00 3.66
473 503 0.321996 GGGGAAAGAGACGAAGCTGT 59.678 55.000 0.00 0.00 0.00 4.40
474 504 0.737715 CGGGGAAAGAGACGAAGCTG 60.738 60.000 0.00 0.00 0.00 4.24
475 505 1.186267 ACGGGGAAAGAGACGAAGCT 61.186 55.000 0.00 0.00 0.00 3.74
476 506 0.736672 GACGGGGAAAGAGACGAAGC 60.737 60.000 0.00 0.00 0.00 3.86
477 507 0.108756 GGACGGGGAAAGAGACGAAG 60.109 60.000 0.00 0.00 0.00 3.79
502 543 0.038892 ATTTTTGCCTCGTGCTGCTG 60.039 50.000 0.00 0.00 42.00 4.41
503 544 1.470098 CTATTTTTGCCTCGTGCTGCT 59.530 47.619 0.00 0.00 42.00 4.24
504 545 1.900237 CTATTTTTGCCTCGTGCTGC 58.100 50.000 0.00 0.00 42.00 5.25
505 546 1.199789 TGCTATTTTTGCCTCGTGCTG 59.800 47.619 1.74 0.00 42.00 4.41
558 606 1.789751 CCGTCTGCGTCTACGTACA 59.210 57.895 4.24 0.00 42.22 2.90
658 739 1.586028 GGTGGTTACCTCGTACGCA 59.414 57.895 11.24 0.00 43.97 5.24
738 828 4.735599 GAGGAGGGGGTTCCGGGT 62.736 72.222 0.00 0.00 42.29 5.28
786 876 2.203972 GATCGTGTTCGGGGTCGTGA 62.204 60.000 0.00 0.00 37.69 4.35
794 884 3.554692 GGCTGCGATCGTGTTCGG 61.555 66.667 17.81 5.95 39.49 4.30
796 886 3.195698 GGGGCTGCGATCGTGTTC 61.196 66.667 17.81 0.00 0.00 3.18
797 887 4.778143 GGGGGCTGCGATCGTGTT 62.778 66.667 17.81 0.00 0.00 3.32
859 949 6.293649 AGGGGATCATATACCAAACCAATT 57.706 37.500 0.00 0.00 33.66 2.32
860 950 5.948481 AGGGGATCATATACCAAACCAAT 57.052 39.130 0.00 0.00 33.66 3.16
861 951 5.435041 AGAAGGGGATCATATACCAAACCAA 59.565 40.000 0.00 0.00 33.66 3.67
862 952 4.981647 AGAAGGGGATCATATACCAAACCA 59.018 41.667 0.00 0.00 33.66 3.67
879 976 4.426313 GGGGCCGGACAAGAAGGG 62.426 72.222 11.00 0.00 0.00 3.95
906 1003 0.796312 GAATCACACGTTCATGCCGT 59.204 50.000 4.66 4.66 39.52 5.68
913 1010 4.876107 AGTATCCAATGGAATCACACGTTC 59.124 41.667 5.89 0.00 34.34 3.95
927 1024 6.516860 GCCACGATGAGTAAGTAGTATCCAAT 60.517 42.308 0.00 0.00 0.00 3.16
989 1086 1.669115 ACACTCATCTGCCACGCAC 60.669 57.895 0.00 0.00 33.79 5.34
1052 1158 1.970917 GAAGGCGGCACAATCAGACG 61.971 60.000 13.08 0.00 0.00 4.18
1117 1233 4.754372 TCAATCAGTCACAAGAACATGC 57.246 40.909 0.00 0.00 0.00 4.06
1118 1234 6.805271 GGAATTCAATCAGTCACAAGAACATG 59.195 38.462 7.93 0.00 0.00 3.21
1119 1235 6.071728 GGGAATTCAATCAGTCACAAGAACAT 60.072 38.462 7.93 0.00 0.00 2.71
1125 1242 3.750371 ACGGGAATTCAATCAGTCACAA 58.250 40.909 7.93 0.00 0.00 3.33
1201 1318 2.667473 ACGATTCCGGGAGTTAACAG 57.333 50.000 8.61 0.00 40.78 3.16
1204 1321 2.364632 TCGTACGATTCCGGGAGTTAA 58.635 47.619 15.28 0.00 40.78 2.01
1240 1357 7.322222 CGATCATCACAAGAGAAGAAACAAAAC 59.678 37.037 0.00 0.00 0.00 2.43
1247 1364 4.389992 GCAACGATCATCACAAGAGAAGAA 59.610 41.667 0.00 0.00 0.00 2.52
1248 1365 3.928992 GCAACGATCATCACAAGAGAAGA 59.071 43.478 0.00 0.00 0.00 2.87
1249 1366 3.681417 TGCAACGATCATCACAAGAGAAG 59.319 43.478 0.00 0.00 0.00 2.85
1266 1383 3.917985 GGGTCGATGTTTACATTTGCAAC 59.082 43.478 0.00 0.00 36.57 4.17
1277 1394 0.252197 GTAGCCCTGGGTCGATGTTT 59.748 55.000 15.56 0.00 0.00 2.83
1286 1403 1.281867 TGACAAAGATGTAGCCCTGGG 59.718 52.381 8.86 8.86 40.74 4.45
1331 1448 4.368315 CGATGACCTATCAATCAACCGAA 58.632 43.478 0.00 0.00 38.69 4.30
1415 1532 4.792068 TGTCTGAATTTTTCACCTCCTGT 58.208 39.130 0.00 0.00 35.46 4.00
1585 1706 3.131850 CCTTGTTGGCCTTGGAGTT 57.868 52.632 3.32 0.00 0.00 3.01
1678 1799 2.719739 CCATGTTCTTCAGGACTGCAT 58.280 47.619 0.00 0.00 0.00 3.96
1679 1800 1.883638 GCCATGTTCTTCAGGACTGCA 60.884 52.381 0.00 0.00 0.00 4.41
1684 1805 3.726557 AAGATGCCATGTTCTTCAGGA 57.273 42.857 0.00 0.00 0.00 3.86
2097 2230 7.189693 TCTTTGTGCACTTAATTAGTCACAG 57.810 36.000 19.41 0.00 41.49 3.66
2106 2239 9.683069 CAGAAGTTAATTCTTTGTGCACTTAAT 57.317 29.630 19.41 9.23 46.49 1.40
2107 2240 8.898761 TCAGAAGTTAATTCTTTGTGCACTTAA 58.101 29.630 19.41 10.23 46.49 1.85
2108 2241 8.445275 TCAGAAGTTAATTCTTTGTGCACTTA 57.555 30.769 19.41 4.09 46.49 2.24
2116 2249 9.447157 AGAGATCCTTCAGAAGTTAATTCTTTG 57.553 33.333 9.41 0.00 46.49 2.77
2117 2250 9.447157 CAGAGATCCTTCAGAAGTTAATTCTTT 57.553 33.333 9.41 0.00 46.49 2.52
2118 2251 8.820831 TCAGAGATCCTTCAGAAGTTAATTCTT 58.179 33.333 9.41 0.00 46.49 2.52
2122 2255 6.991531 GCATCAGAGATCCTTCAGAAGTTAAT 59.008 38.462 9.41 0.09 0.00 1.40
2123 2256 6.070596 TGCATCAGAGATCCTTCAGAAGTTAA 60.071 38.462 9.41 0.00 0.00 2.01
2128 2261 3.431905 GCTGCATCAGAGATCCTTCAGAA 60.432 47.826 0.00 0.00 32.44 3.02
2129 2262 2.102757 GCTGCATCAGAGATCCTTCAGA 59.897 50.000 0.00 0.00 32.44 3.27
2132 2265 2.616634 TGCTGCATCAGAGATCCTTC 57.383 50.000 0.00 0.00 32.44 3.46
2136 2269 3.478509 AGGAAATGCTGCATCAGAGATC 58.521 45.455 16.55 7.58 32.44 2.75
2137 2270 3.579534 AGGAAATGCTGCATCAGAGAT 57.420 42.857 16.55 0.00 32.44 2.75
2141 2274 3.014623 TCAGAAGGAAATGCTGCATCAG 58.985 45.455 16.55 0.08 34.12 2.90
2149 2282 3.254166 TGCTCAAGTTCAGAAGGAAATGC 59.746 43.478 0.00 0.00 37.23 3.56
2471 2635 3.242969 GCACATAACCATGTCAGATGCTG 60.243 47.826 0.00 0.00 43.73 4.41
2485 2649 7.919091 ACAATGAATGAATGATCTGCACATAAC 59.081 33.333 0.00 0.00 0.00 1.89
2498 2662 6.954616 TTGCTGCTTTACAATGAATGAATG 57.045 33.333 0.00 0.00 0.00 2.67
2509 2691 4.983538 CACACATTCATTTGCTGCTTTACA 59.016 37.500 0.00 0.00 0.00 2.41
2611 2793 0.512518 CTTGTGATTTCAGCGTCGCA 59.487 50.000 21.09 0.00 33.42 5.10
2625 2807 0.596082 CCTACAAAACGGGCCTTGTG 59.404 55.000 17.25 10.97 36.47 3.33
2652 2834 2.035442 GTTTGAGACGAGCCCTGCC 61.035 63.158 0.00 0.00 0.00 4.85
2683 2949 1.140452 TCATCAGATGCTCAGGAAGGC 59.860 52.381 5.41 0.00 0.00 4.35
2699 2965 4.324267 TCAGACCATGCATCATCATCATC 58.676 43.478 0.00 0.00 0.00 2.92
2700 2966 4.327680 CTCAGACCATGCATCATCATCAT 58.672 43.478 0.00 0.00 0.00 2.45
2820 3092 8.702438 CATTTATCAGAAACCACAATGTGTTTC 58.298 33.333 22.07 22.07 35.71 2.78
2876 3148 0.454957 GCTCGTCGTAGCACCGTTAA 60.455 55.000 10.53 0.00 42.30 2.01
2878 3150 2.126580 GCTCGTCGTAGCACCGTT 60.127 61.111 10.53 0.00 42.30 4.44
2911 3183 6.655848 TGTACTCCGGTTTATTAATGCAAAGT 59.344 34.615 0.00 0.00 0.00 2.66
2929 3201 9.953697 CAATCTACTCTACTGTAAATGTACTCC 57.046 37.037 0.00 0.00 0.00 3.85
2944 3216 3.419974 TCCCTACCCCCAATCTACTCTA 58.580 50.000 0.00 0.00 0.00 2.43
3106 3387 1.984066 ACTGGATAGGAGTAGCGACC 58.016 55.000 0.00 0.00 0.00 4.79
3141 3422 7.567622 TCTGTTTGGTATTAGGCCTAGACTATT 59.432 37.037 20.51 5.24 0.00 1.73
3363 3644 2.103042 GCTGTCTGGCATCGTGGTC 61.103 63.158 0.00 0.00 0.00 4.02
3406 3687 1.605457 GCTTCACGTCAGATGTGTGGA 60.605 52.381 20.19 8.73 36.53 4.02
3548 3831 2.234896 TCATGTGTCGTTACCCCCTA 57.765 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.