Multiple sequence alignment - TraesCS5A01G371100

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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 TraesCS5A01G371100 chr5A 100.000 3658 0 0 1 3658 570183882 570187539 0.000000e+00 6756
1 TraesCS5A01G371100 chr5A 79.429 175 35 1 3085 3259 522110414 522110241 4.960000e-24 122
2 TraesCS5A01G371100 chr3B 89.728 3495 268 45 178 3658 232607878 232604461 0.000000e+00 4381
3 TraesCS5A01G371100 chr3B 77.143 175 39 1 3085 3259 525238498 525238671 2.320000e-17 100
4 TraesCS5A01G371100 chr1B 91.622 2769 178 36 181 2938 662072668 662069943 0.000000e+00 3779
5 TraesCS5A01G371100 chr1B 95.461 727 31 1 2932 3658 662069901 662069177 0.000000e+00 1158
6 TraesCS5A01G371100 chr2B 91.745 1272 93 7 1694 2957 11911268 11910001 0.000000e+00 1757
7 TraesCS5A01G371100 chr2B 88.021 960 93 11 693 1649 11912223 11911283 0.000000e+00 1116
8 TraesCS5A01G371100 chr2B 78.644 1475 266 34 2217 3658 259764130 259762672 0.000000e+00 933
9 TraesCS5A01G371100 chr2B 87.815 476 31 8 179 642 11912694 11912234 1.930000e-147 532
10 TraesCS5A01G371100 chr2B 72.202 554 142 10 2724 3270 794928126 794928674 3.780000e-35 159
11 TraesCS5A01G371100 chr2B 97.802 91 2 0 2927 3017 11910003 11909913 1.360000e-34 158
12 TraesCS5A01G371100 chrUn 79.973 1483 246 35 2210 3658 24278235 24276770 0.000000e+00 1046
13 TraesCS5A01G371100 chr2D 79.932 1480 252 32 2210 3658 431389059 431390524 0.000000e+00 1046
14 TraesCS5A01G371100 chr7A 79.164 1483 258 35 2210 3658 675508908 675507443 0.000000e+00 979
15 TraesCS5A01G371100 chr7A 84.936 551 80 3 2752 3300 102077629 102077080 4.130000e-154 555
16 TraesCS5A01G371100 chr7D 88.306 248 29 0 3411 3658 86060105 86060352 7.680000e-77 298
17 TraesCS5A01G371100 chr5D 83.735 166 19 6 10 169 216093896 216093733 2.280000e-32 150
18 TraesCS5A01G371100 chr5D 86.458 96 13 0 3085 3180 432216288 432216383 5.000000e-19 106
19 TraesCS5A01G371100 chr4A 82.456 171 26 4 12 179 518976495 518976664 2.940000e-31 147
20 TraesCS5A01G371100 chr3D 81.757 148 23 4 35 180 75561909 75562054 1.780000e-23 121
21 TraesCS5A01G371100 chr4B 78.286 175 37 1 3085 3259 618615777 618615950 1.070000e-20 111
22 TraesCS5A01G371100 chr3A 80.137 146 27 2 35 178 89675326 89675471 1.390000e-19 108


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 TraesCS5A01G371100 chr5A 570183882 570187539 3657 False 6756.00 6756 100.00000 1 3658 1 chr5A.!!$F1 3657
1 TraesCS5A01G371100 chr3B 232604461 232607878 3417 True 4381.00 4381 89.72800 178 3658 1 chr3B.!!$R1 3480
2 TraesCS5A01G371100 chr1B 662069177 662072668 3491 True 2468.50 3779 93.54150 181 3658 2 chr1B.!!$R1 3477
3 TraesCS5A01G371100 chr2B 259762672 259764130 1458 True 933.00 933 78.64400 2217 3658 1 chr2B.!!$R1 1441
4 TraesCS5A01G371100 chr2B 11909913 11912694 2781 True 890.75 1757 91.34575 179 3017 4 chr2B.!!$R2 2838
5 TraesCS5A01G371100 chrUn 24276770 24278235 1465 True 1046.00 1046 79.97300 2210 3658 1 chrUn.!!$R1 1448
6 TraesCS5A01G371100 chr2D 431389059 431390524 1465 False 1046.00 1046 79.93200 2210 3658 1 chr2D.!!$F1 1448
7 TraesCS5A01G371100 chr7A 675507443 675508908 1465 True 979.00 979 79.16400 2210 3658 1 chr7A.!!$R2 1448
8 TraesCS5A01G371100 chr7A 102077080 102077629 549 True 555.00 555 84.93600 2752 3300 1 chr7A.!!$R1 548

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
913 931 0.10412 CGATGAGCGTCCCAACCATA 59.896 55.0 0.00 0.0 34.64 2.74 F
2015 2035 0.16747 CAACACCTTCATGCGAGCAG 59.833 55.0 3.58 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2169 0.042188 CACACACCGAAAGCAAGACG 60.042 55.0 0.0 0.0 0.0 4.18 R
3479 3618 0.608130 CACACCCATCGACTCCTTCA 59.392 55.0 0.0 0.0 0.0 3.02 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
25 26 7.383102 ACAAATCATGATTGAGTACTGGAAC 57.617 36.000 21.39 0.00 34.73 3.62
26 27 6.942005 ACAAATCATGATTGAGTACTGGAACA 59.058 34.615 21.39 0.00 34.73 3.18
27 28 7.448161 ACAAATCATGATTGAGTACTGGAACAA 59.552 33.333 21.39 0.00 33.91 2.83
28 29 8.298854 CAAATCATGATTGAGTACTGGAACAAA 58.701 33.333 21.39 0.00 33.91 2.83
29 30 6.801539 TCATGATTGAGTACTGGAACAAAC 57.198 37.500 0.00 0.00 38.70 2.93
30 31 6.533730 TCATGATTGAGTACTGGAACAAACT 58.466 36.000 0.00 0.00 38.70 2.66
31 32 6.650807 TCATGATTGAGTACTGGAACAAACTC 59.349 38.462 0.00 0.00 45.84 3.01
32 33 6.174720 TGATTGAGTACTGGAACAAACTCT 57.825 37.500 0.00 0.00 45.84 3.24
33 34 6.591935 TGATTGAGTACTGGAACAAACTCTT 58.408 36.000 0.00 0.00 45.84 2.85
34 35 7.732025 TGATTGAGTACTGGAACAAACTCTTA 58.268 34.615 0.00 3.14 45.84 2.10
35 36 8.208224 TGATTGAGTACTGGAACAAACTCTTAA 58.792 33.333 0.00 2.17 45.84 1.85
36 37 8.608844 ATTGAGTACTGGAACAAACTCTTAAG 57.391 34.615 0.00 0.00 45.84 1.85
37 38 7.120923 TGAGTACTGGAACAAACTCTTAAGT 57.879 36.000 0.00 0.00 45.84 2.24
38 39 8.241497 TGAGTACTGGAACAAACTCTTAAGTA 57.759 34.615 0.00 0.00 45.84 2.24
39 40 8.698210 TGAGTACTGGAACAAACTCTTAAGTAA 58.302 33.333 0.00 0.00 45.84 2.24
40 41 9.538508 GAGTACTGGAACAAACTCTTAAGTAAA 57.461 33.333 0.00 0.00 43.73 2.01
91 92 6.798427 ATTAGAGTGACTAATGGAGAAGCA 57.202 37.500 0.00 0.00 46.26 3.91
92 93 4.734398 AGAGTGACTAATGGAGAAGCAG 57.266 45.455 0.00 0.00 0.00 4.24
93 94 4.348486 AGAGTGACTAATGGAGAAGCAGA 58.652 43.478 0.00 0.00 0.00 4.26
94 95 4.402155 AGAGTGACTAATGGAGAAGCAGAG 59.598 45.833 0.00 0.00 0.00 3.35
95 96 3.450457 AGTGACTAATGGAGAAGCAGAGG 59.550 47.826 0.00 0.00 0.00 3.69
96 97 3.449018 GTGACTAATGGAGAAGCAGAGGA 59.551 47.826 0.00 0.00 0.00 3.71
97 98 3.703556 TGACTAATGGAGAAGCAGAGGAG 59.296 47.826 0.00 0.00 0.00 3.69
98 99 3.704061 GACTAATGGAGAAGCAGAGGAGT 59.296 47.826 0.00 0.00 0.00 3.85
99 100 4.873010 ACTAATGGAGAAGCAGAGGAGTA 58.127 43.478 0.00 0.00 0.00 2.59
100 101 5.273208 ACTAATGGAGAAGCAGAGGAGTAA 58.727 41.667 0.00 0.00 0.00 2.24
101 102 4.751767 AATGGAGAAGCAGAGGAGTAAG 57.248 45.455 0.00 0.00 0.00 2.34
102 103 2.461695 TGGAGAAGCAGAGGAGTAAGG 58.538 52.381 0.00 0.00 0.00 2.69
103 104 2.225394 TGGAGAAGCAGAGGAGTAAGGT 60.225 50.000 0.00 0.00 0.00 3.50
104 105 2.167487 GGAGAAGCAGAGGAGTAAGGTG 59.833 54.545 0.00 0.00 0.00 4.00
105 106 2.829120 GAGAAGCAGAGGAGTAAGGTGT 59.171 50.000 0.00 0.00 0.00 4.16
106 107 3.243724 AGAAGCAGAGGAGTAAGGTGTT 58.756 45.455 0.00 0.00 0.00 3.32
107 108 3.259625 AGAAGCAGAGGAGTAAGGTGTTC 59.740 47.826 0.00 0.00 0.00 3.18
108 109 2.896039 AGCAGAGGAGTAAGGTGTTCT 58.104 47.619 0.00 0.00 0.00 3.01
109 110 2.829120 AGCAGAGGAGTAAGGTGTTCTC 59.171 50.000 0.00 0.00 0.00 2.87
110 111 2.563179 GCAGAGGAGTAAGGTGTTCTCA 59.437 50.000 0.00 0.00 0.00 3.27
111 112 3.367910 GCAGAGGAGTAAGGTGTTCTCAG 60.368 52.174 0.00 0.00 0.00 3.35
112 113 3.194542 CAGAGGAGTAAGGTGTTCTCAGG 59.805 52.174 0.00 0.00 0.00 3.86
113 114 2.498078 GAGGAGTAAGGTGTTCTCAGGG 59.502 54.545 0.00 0.00 0.00 4.45
114 115 2.111972 AGGAGTAAGGTGTTCTCAGGGA 59.888 50.000 0.00 0.00 0.00 4.20
115 116 2.498078 GGAGTAAGGTGTTCTCAGGGAG 59.502 54.545 0.00 0.00 0.00 4.30
116 117 3.166679 GAGTAAGGTGTTCTCAGGGAGT 58.833 50.000 0.00 0.00 0.00 3.85
117 118 3.579151 GAGTAAGGTGTTCTCAGGGAGTT 59.421 47.826 0.00 0.00 0.00 3.01
118 119 3.974642 AGTAAGGTGTTCTCAGGGAGTTT 59.025 43.478 0.00 0.00 0.00 2.66
119 120 2.938956 AGGTGTTCTCAGGGAGTTTG 57.061 50.000 0.00 0.00 0.00 2.93
120 121 1.421646 AGGTGTTCTCAGGGAGTTTGG 59.578 52.381 0.00 0.00 0.00 3.28
121 122 1.420138 GGTGTTCTCAGGGAGTTTGGA 59.580 52.381 0.00 0.00 0.00 3.53
122 123 2.158667 GGTGTTCTCAGGGAGTTTGGAA 60.159 50.000 0.00 0.00 0.00 3.53
123 124 3.498661 GGTGTTCTCAGGGAGTTTGGAAT 60.499 47.826 0.00 0.00 0.00 3.01
124 125 3.753797 GTGTTCTCAGGGAGTTTGGAATC 59.246 47.826 0.00 0.00 0.00 2.52
125 126 3.244911 TGTTCTCAGGGAGTTTGGAATCC 60.245 47.826 0.00 0.00 34.64 3.01
132 133 2.820178 GGAGTTTGGAATCCCCATTGT 58.180 47.619 0.00 0.00 46.10 2.71
133 134 3.976015 GGAGTTTGGAATCCCCATTGTA 58.024 45.455 0.00 0.00 46.10 2.41
134 135 4.546674 GGAGTTTGGAATCCCCATTGTAT 58.453 43.478 0.00 0.00 46.10 2.29
135 136 4.342092 GGAGTTTGGAATCCCCATTGTATG 59.658 45.833 0.00 0.00 46.10 2.39
136 137 4.946646 AGTTTGGAATCCCCATTGTATGT 58.053 39.130 0.00 0.00 46.10 2.29
137 138 5.341169 AGTTTGGAATCCCCATTGTATGTT 58.659 37.500 0.00 0.00 46.10 2.71
138 139 5.784906 AGTTTGGAATCCCCATTGTATGTTT 59.215 36.000 0.00 0.00 46.10 2.83
139 140 5.930837 TTGGAATCCCCATTGTATGTTTC 57.069 39.130 0.00 0.00 46.10 2.78
140 141 5.205517 TGGAATCCCCATTGTATGTTTCT 57.794 39.130 0.00 0.00 40.82 2.52
141 142 6.334378 TGGAATCCCCATTGTATGTTTCTA 57.666 37.500 0.00 0.00 40.82 2.10
142 143 6.364701 TGGAATCCCCATTGTATGTTTCTAG 58.635 40.000 0.00 0.00 40.82 2.43
143 144 5.241728 GGAATCCCCATTGTATGTTTCTAGC 59.758 44.000 0.00 0.00 34.14 3.42
144 145 4.853468 TCCCCATTGTATGTTTCTAGCA 57.147 40.909 0.00 0.00 0.00 3.49
145 146 4.523083 TCCCCATTGTATGTTTCTAGCAC 58.477 43.478 0.00 0.00 0.00 4.40
146 147 4.018870 TCCCCATTGTATGTTTCTAGCACA 60.019 41.667 0.00 0.00 0.00 4.57
147 148 4.096382 CCCCATTGTATGTTTCTAGCACAC 59.904 45.833 0.00 0.00 0.00 3.82
148 149 4.096382 CCCATTGTATGTTTCTAGCACACC 59.904 45.833 0.00 0.00 0.00 4.16
149 150 4.943705 CCATTGTATGTTTCTAGCACACCT 59.056 41.667 0.00 0.00 0.00 4.00
150 151 6.112734 CCATTGTATGTTTCTAGCACACCTA 58.887 40.000 0.00 0.00 0.00 3.08
151 152 6.767902 CCATTGTATGTTTCTAGCACACCTAT 59.232 38.462 0.00 0.00 0.00 2.57
152 153 7.254898 CCATTGTATGTTTCTAGCACACCTATG 60.255 40.741 0.00 4.70 0.00 2.23
153 154 6.294361 TGTATGTTTCTAGCACACCTATGT 57.706 37.500 0.00 0.00 40.80 2.29
154 155 7.412853 TGTATGTTTCTAGCACACCTATGTA 57.587 36.000 0.00 0.00 36.72 2.29
155 156 8.018537 TGTATGTTTCTAGCACACCTATGTAT 57.981 34.615 0.00 0.00 36.72 2.29
156 157 9.138596 TGTATGTTTCTAGCACACCTATGTATA 57.861 33.333 0.00 0.00 36.72 1.47
157 158 9.627395 GTATGTTTCTAGCACACCTATGTATAG 57.373 37.037 0.00 0.00 36.72 1.31
158 159 7.655521 TGTTTCTAGCACACCTATGTATAGT 57.344 36.000 0.00 0.00 36.72 2.12
159 160 7.713750 TGTTTCTAGCACACCTATGTATAGTC 58.286 38.462 0.00 0.00 36.72 2.59
160 161 7.340999 TGTTTCTAGCACACCTATGTATAGTCA 59.659 37.037 0.00 0.00 36.72 3.41
161 162 8.361139 GTTTCTAGCACACCTATGTATAGTCAT 58.639 37.037 0.00 0.00 36.72 3.06
162 163 9.582648 TTTCTAGCACACCTATGTATAGTCATA 57.417 33.333 0.00 0.00 36.72 2.15
163 164 8.794335 TCTAGCACACCTATGTATAGTCATAG 57.206 38.462 6.71 6.71 43.81 2.23
164 165 8.383947 TCTAGCACACCTATGTATAGTCATAGT 58.616 37.037 11.16 0.48 43.12 2.12
165 166 9.668497 CTAGCACACCTATGTATAGTCATAGTA 57.332 37.037 11.16 0.00 43.12 1.82
167 168 8.961634 AGCACACCTATGTATAGTCATAGTATG 58.038 37.037 3.55 3.55 43.12 2.39
168 169 8.191446 GCACACCTATGTATAGTCATAGTATGG 58.809 40.741 10.26 0.00 43.12 2.74
169 170 9.462606 CACACCTATGTATAGTCATAGTATGGA 57.537 37.037 10.26 0.00 43.12 3.41
170 171 9.688091 ACACCTATGTATAGTCATAGTATGGAG 57.312 37.037 10.26 0.00 43.12 3.86
171 172 9.688091 CACCTATGTATAGTCATAGTATGGAGT 57.312 37.037 10.26 3.40 43.12 3.85
172 173 9.688091 ACCTATGTATAGTCATAGTATGGAGTG 57.312 37.037 10.26 0.00 43.12 3.51
173 174 9.126151 CCTATGTATAGTCATAGTATGGAGTGG 57.874 40.741 10.26 0.00 43.12 4.00
174 175 9.688091 CTATGTATAGTCATAGTATGGAGTGGT 57.312 37.037 10.26 0.00 41.08 4.16
176 177 8.859236 TGTATAGTCATAGTATGGAGTGGTAC 57.141 38.462 10.26 7.15 0.00 3.34
201 202 2.264461 TGCGAATTTTCAGCGGCCA 61.264 52.632 2.24 0.00 32.24 5.36
270 271 2.122989 ACTCGGTCAGTGGGTGGT 60.123 61.111 0.00 0.00 32.26 4.16
292 293 1.068127 GGCCTAGCGAAAGGAATACGA 59.932 52.381 7.61 0.00 39.15 3.43
310 311 2.995574 CCCGGGATACGCCTAGGG 60.996 72.222 18.48 3.13 44.12 3.53
350 351 2.120909 CGGCCCATTGCTCGGAAAT 61.121 57.895 0.00 0.00 40.92 2.17
403 404 2.917713 TAGGCCCATGACCATTGTTT 57.082 45.000 0.00 0.00 0.00 2.83
420 421 6.532657 CCATTGTTTGAAATAGCACAGAATCC 59.467 38.462 0.00 0.00 0.00 3.01
483 491 2.413837 CGTGGAGTAAACCAGAACCAG 58.586 52.381 0.00 0.00 40.85 4.00
523 531 3.624777 CAGGGAAAATATCTGGTGCACT 58.375 45.455 17.98 0.00 0.00 4.40
529 537 0.179073 ATATCTGGTGCACTGCCGAC 60.179 55.000 17.98 0.00 0.00 4.79
556 570 2.115973 TCCATCCCCATCTCCATCCATA 59.884 50.000 0.00 0.00 0.00 2.74
571 585 3.224324 ATATGGCTCGACCGCGGT 61.224 61.111 34.89 34.89 43.94 5.68
608 622 0.842635 GAGACTTGCTCCATCCCCAT 59.157 55.000 0.00 0.00 37.69 4.00
666 680 4.383052 GCCGTCGTGATATCTACTTGATTG 59.617 45.833 3.98 0.00 36.65 2.67
687 701 1.079405 GTCTCCATCCGTTTGCCGA 60.079 57.895 0.00 0.00 39.56 5.54
753 771 7.349645 CGAGCTCGATGGGTATGATTACCAT 62.350 48.000 32.06 0.00 44.94 3.55
773 791 1.355381 TGGTCCCTGCATCATGTTTCT 59.645 47.619 0.00 0.00 0.00 2.52
774 792 2.225091 TGGTCCCTGCATCATGTTTCTT 60.225 45.455 0.00 0.00 0.00 2.52
775 793 3.010027 TGGTCCCTGCATCATGTTTCTTA 59.990 43.478 0.00 0.00 0.00 2.10
776 794 4.016444 GGTCCCTGCATCATGTTTCTTAA 58.984 43.478 0.00 0.00 0.00 1.85
784 802 7.816031 CCTGCATCATGTTTCTTAATTTTCTGT 59.184 33.333 0.00 0.00 0.00 3.41
794 812 4.748102 TCTTAATTTTCTGTCGCGTGTTCT 59.252 37.500 5.77 0.00 0.00 3.01
797 815 1.929230 TTTCTGTCGCGTGTTCTTCA 58.071 45.000 5.77 0.00 0.00 3.02
819 837 4.806247 CAGATTTCTTACTAGTTGCCTCCG 59.194 45.833 0.00 0.00 0.00 4.63
820 838 4.710375 AGATTTCTTACTAGTTGCCTCCGA 59.290 41.667 0.00 0.00 0.00 4.55
821 839 5.364157 AGATTTCTTACTAGTTGCCTCCGAT 59.636 40.000 0.00 0.00 0.00 4.18
823 841 4.386867 TCTTACTAGTTGCCTCCGATTG 57.613 45.455 0.00 0.00 0.00 2.67
824 842 2.596904 TACTAGTTGCCTCCGATTGC 57.403 50.000 0.00 0.00 0.00 3.56
832 850 3.144657 TGCCTCCGATTGCATTCATAT 57.855 42.857 9.14 0.00 31.31 1.78
836 854 4.623886 GCCTCCGATTGCATTCATATAGGA 60.624 45.833 9.14 3.62 0.00 2.94
845 863 5.379187 TGCATTCATATAGGATGTGTGCTT 58.621 37.500 12.49 0.00 34.34 3.91
879 897 0.613260 AACAACTGCGCCTATCCAGA 59.387 50.000 4.18 0.00 33.40 3.86
886 904 0.676184 GCGCCTATCCAGATGAGTCA 59.324 55.000 0.00 0.00 0.00 3.41
913 931 0.104120 CGATGAGCGTCCCAACCATA 59.896 55.000 0.00 0.00 34.64 2.74
914 932 1.583054 GATGAGCGTCCCAACCATAC 58.417 55.000 0.00 0.00 0.00 2.39
986 1005 1.748493 GGTGTGTTCTGAAGCAACCAA 59.252 47.619 9.34 0.00 0.00 3.67
1001 1020 3.594568 CAATGGCTGGACACGCAT 58.405 55.556 0.00 0.00 0.00 4.73
1017 1036 3.052036 ACGCATGTCAGTGAAAAATTGC 58.948 40.909 0.00 0.00 0.00 3.56
1131 1150 4.565022 AGAAGTGTGTTGTTTTTGTTGGG 58.435 39.130 0.00 0.00 0.00 4.12
1139 1158 4.887655 TGTTGTTTTTGTTGGGTTTGGTTT 59.112 33.333 0.00 0.00 0.00 3.27
1142 1161 5.316987 TGTTTTTGTTGGGTTTGGTTTGAT 58.683 33.333 0.00 0.00 0.00 2.57
1152 1171 4.427312 GGTTTGGTTTGATGATCTGATGC 58.573 43.478 0.00 0.00 0.00 3.91
1167 1186 6.948309 TGATCTGATGCTAGCATTAGGTAGTA 59.052 38.462 35.72 23.22 45.40 1.82
1195 1214 6.932901 ACATAATTTGATGCAGTTTGTTCG 57.067 33.333 0.00 0.00 0.00 3.95
1222 1241 8.837788 TTTTATTGATGATCTGATCGTAGCAT 57.162 30.769 12.15 7.50 0.00 3.79
1248 1267 2.306847 AGTAAACTGCAACTGGTTGGG 58.693 47.619 14.17 0.00 40.74 4.12
1278 1297 8.591940 TGTTGGATTTTATTGATGATTTGGTGA 58.408 29.630 0.00 0.00 0.00 4.02
1324 1343 1.211949 GGCTGGAGCTTGTTGGGTATA 59.788 52.381 0.00 0.00 41.70 1.47
1352 1371 4.811555 TGCAGTGACTTATGTTGTGTTC 57.188 40.909 0.00 0.00 0.00 3.18
1355 1374 5.207768 GCAGTGACTTATGTTGTGTTCTTG 58.792 41.667 0.00 0.00 0.00 3.02
1356 1375 5.007626 GCAGTGACTTATGTTGTGTTCTTGA 59.992 40.000 0.00 0.00 0.00 3.02
1364 1383 8.902806 ACTTATGTTGTGTTCTTGAGATGAAAA 58.097 29.630 0.00 0.00 0.00 2.29
1368 1387 8.275015 TGTTGTGTTCTTGAGATGAAAAGTTA 57.725 30.769 0.00 0.00 0.00 2.24
1443 1462 6.431234 GTGATGGTCTTGGATTTCTAGTTTGT 59.569 38.462 0.00 0.00 0.00 2.83
1445 1464 7.505585 TGATGGTCTTGGATTTCTAGTTTGTTT 59.494 33.333 0.00 0.00 0.00 2.83
1447 1466 8.391075 TGGTCTTGGATTTCTAGTTTGTTTAG 57.609 34.615 0.00 0.00 0.00 1.85
1450 1469 9.274206 GTCTTGGATTTCTAGTTTGTTTAGAGT 57.726 33.333 0.00 0.00 0.00 3.24
1470 1489 5.072600 AGAGTACATTGGAGTTTTGTGGGTA 59.927 40.000 0.00 0.00 0.00 3.69
1475 1494 3.168035 TGGAGTTTTGTGGGTATGCAT 57.832 42.857 3.79 3.79 0.00 3.96
1504 1523 1.913262 TGTGTGGGCATCGGAGAGT 60.913 57.895 0.00 0.00 43.63 3.24
1505 1524 1.153549 GTGTGGGCATCGGAGAGTC 60.154 63.158 0.00 0.00 43.63 3.36
1520 1539 3.603532 GAGAGTCTGTGCCATCATTGAA 58.396 45.455 0.00 0.00 0.00 2.69
1535 1554 6.183360 CCATCATTGAATTTAGGATGGCTTGT 60.183 38.462 16.97 0.00 45.85 3.16
1538 1557 5.404466 TTGAATTTAGGATGGCTTGTTGG 57.596 39.130 0.00 0.00 0.00 3.77
1547 1566 3.195396 GGATGGCTTGTTGGATTAGCAAA 59.805 43.478 0.00 0.00 36.64 3.68
1567 1586 3.649277 CTTGACCGCGGAGGACTGG 62.649 68.421 35.90 10.80 45.00 4.00
1613 1633 7.132694 TGCAGTGACTTATATTGTGTTCTTG 57.867 36.000 0.00 0.00 0.00 3.02
1627 1647 6.757897 TGTGTTCTTGAGATGAAAAGTTGT 57.242 33.333 0.00 0.00 0.00 3.32
1651 1671 9.365906 TGTATTAGGGAGTTTAATACGGATGTA 57.634 33.333 9.36 0.00 42.67 2.29
1654 1674 8.537728 TTAGGGAGTTTAATACGGATGTAAGA 57.462 34.615 0.00 0.00 33.44 2.10
1655 1675 7.427989 AGGGAGTTTAATACGGATGTAAGAA 57.572 36.000 0.00 0.00 33.44 2.52
1659 1679 8.121086 GGAGTTTAATACGGATGTAAGAAAAGC 58.879 37.037 0.00 0.00 33.44 3.51
1660 1680 7.681903 AGTTTAATACGGATGTAAGAAAAGCG 58.318 34.615 0.00 0.00 33.44 4.68
1665 1685 4.563061 ACGGATGTAAGAAAAGCGTTAGT 58.437 39.130 0.00 0.00 0.00 2.24
1666 1686 4.387862 ACGGATGTAAGAAAAGCGTTAGTG 59.612 41.667 0.00 0.00 0.00 2.74
1667 1687 4.624024 CGGATGTAAGAAAAGCGTTAGTGA 59.376 41.667 0.00 0.00 0.00 3.41
1668 1688 5.291128 CGGATGTAAGAAAAGCGTTAGTGAT 59.709 40.000 0.00 0.00 0.00 3.06
1670 1690 7.009815 CGGATGTAAGAAAAGCGTTAGTGATAA 59.990 37.037 0.00 0.00 0.00 1.75
1671 1691 8.827677 GGATGTAAGAAAAGCGTTAGTGATAAT 58.172 33.333 0.00 0.00 0.00 1.28
1673 1693 8.766000 TGTAAGAAAAGCGTTAGTGATAATGA 57.234 30.769 0.00 0.00 0.00 2.57
1674 1694 8.869897 TGTAAGAAAAGCGTTAGTGATAATGAG 58.130 33.333 0.00 0.00 0.00 2.90
1675 1695 6.910536 AGAAAAGCGTTAGTGATAATGAGG 57.089 37.500 0.00 0.00 0.00 3.86
1676 1696 6.407202 AGAAAAGCGTTAGTGATAATGAGGT 58.593 36.000 0.00 0.00 0.00 3.85
1677 1697 7.553334 AGAAAAGCGTTAGTGATAATGAGGTA 58.447 34.615 0.00 0.00 0.00 3.08
1678 1698 8.204836 AGAAAAGCGTTAGTGATAATGAGGTAT 58.795 33.333 0.00 0.00 0.00 2.73
1679 1699 9.472361 GAAAAGCGTTAGTGATAATGAGGTATA 57.528 33.333 0.00 0.00 0.00 1.47
1680 1700 9.998106 AAAAGCGTTAGTGATAATGAGGTATAT 57.002 29.630 0.00 0.00 0.00 0.86
1681 1701 9.998106 AAAGCGTTAGTGATAATGAGGTATATT 57.002 29.630 0.00 0.00 0.00 1.28
1690 1710 9.836864 GTGATAATGAGGTATATTATGATGGCA 57.163 33.333 0.00 0.00 32.42 4.92
1695 1715 6.950842 TGAGGTATATTATGATGGCAGAAGG 58.049 40.000 0.00 0.00 0.00 3.46
1696 1716 6.501805 TGAGGTATATTATGATGGCAGAAGGT 59.498 38.462 0.00 0.00 0.00 3.50
1697 1717 7.017551 TGAGGTATATTATGATGGCAGAAGGTT 59.982 37.037 0.00 0.00 0.00 3.50
1698 1718 7.170965 AGGTATATTATGATGGCAGAAGGTTG 58.829 38.462 0.00 0.00 0.00 3.77
1699 1719 6.375455 GGTATATTATGATGGCAGAAGGTTGG 59.625 42.308 0.00 0.00 0.00 3.77
1700 1720 3.737559 TTATGATGGCAGAAGGTTGGT 57.262 42.857 0.00 0.00 0.00 3.67
1701 1721 1.843368 ATGATGGCAGAAGGTTGGTG 58.157 50.000 0.00 0.00 0.00 4.17
1702 1722 0.478072 TGATGGCAGAAGGTTGGTGT 59.522 50.000 0.00 0.00 0.00 4.16
1709 1729 2.586425 CAGAAGGTTGGTGTGTTGGAT 58.414 47.619 0.00 0.00 0.00 3.41
1756 1776 2.131183 GTTTTGTGGCTGCGCAATTTA 58.869 42.857 13.05 0.00 0.00 1.40
1779 1799 1.457455 GGTGTATGGGCATTGGGGG 60.457 63.158 0.00 0.00 0.00 5.40
1780 1800 1.618030 GTGTATGGGCATTGGGGGA 59.382 57.895 0.00 0.00 0.00 4.81
1802 1822 6.444633 GGATCTGTGCCATGATTGAATTTAG 58.555 40.000 0.00 0.00 0.00 1.85
1809 1829 6.041296 GTGCCATGATTGAATTTAGGAGGAAT 59.959 38.462 0.00 0.00 0.00 3.01
1810 1830 6.612456 TGCCATGATTGAATTTAGGAGGAATT 59.388 34.615 0.00 0.00 0.00 2.17
1831 1851 2.018542 TTGTCGCCTGGTGCTATTAC 57.981 50.000 1.39 0.00 38.05 1.89
1841 1861 5.454187 GCCTGGTGCTATTACTGGTATACAA 60.454 44.000 5.01 0.00 36.87 2.41
1842 1862 6.223852 CCTGGTGCTATTACTGGTATACAAG 58.776 44.000 5.66 5.66 0.00 3.16
1885 1905 2.037251 CGATCGATTGGGTGGGTTAGAT 59.963 50.000 10.26 0.00 0.00 1.98
1893 1913 8.537016 TCGATTGGGTGGGTTAGATTTATATAG 58.463 37.037 0.00 0.00 0.00 1.31
1921 1941 7.354025 TGCTGCAAAAACATTTCTTGATATG 57.646 32.000 0.00 0.68 0.00 1.78
1954 1974 3.117794 CAGCTGTGTTGGATTGTTTGTG 58.882 45.455 5.25 0.00 0.00 3.33
1975 1995 6.754193 TGTGATGTGTGTTGAGTATAGTCAA 58.246 36.000 17.33 17.33 33.95 3.18
1980 2000 5.178797 GTGTGTTGAGTATAGTCAATGGCT 58.821 41.667 22.65 0.00 38.68 4.75
1983 2003 3.475566 TGAGTATAGTCAATGGCTGGC 57.524 47.619 7.84 0.00 0.00 4.85
1988 2008 0.546122 TAGTCAATGGCTGGCCGATT 59.454 50.000 0.00 5.50 39.42 3.34
2006 2026 5.583495 CCGATTGTTTTTACAACACCTTCA 58.417 37.500 0.00 0.00 31.89 3.02
2015 2035 0.167470 CAACACCTTCATGCGAGCAG 59.833 55.000 3.58 0.00 0.00 4.24
2026 2046 2.664851 CGAGCAGGTCGCCACAAA 60.665 61.111 9.46 0.00 43.03 2.83
2065 2085 5.545658 AGATGCTGTAATTGGTTGTTACG 57.454 39.130 0.00 0.00 35.35 3.18
2094 2114 7.485277 TCCGGTTAATTATGTAATTGCAAAACG 59.515 33.333 1.71 4.44 36.62 3.60
2099 2119 9.862371 TTAATTATGTAATTGCAAAACGATGGT 57.138 25.926 1.71 0.00 36.62 3.55
2127 2147 0.761802 TGTATGGTGAGTGTGTGGCA 59.238 50.000 0.00 0.00 0.00 4.92
2128 2148 1.141858 TGTATGGTGAGTGTGTGGCAA 59.858 47.619 0.00 0.00 0.00 4.52
2148 2169 4.448732 GCAACTGTGAACATGAAAAATCCC 59.551 41.667 0.00 0.00 0.00 3.85
2160 2181 2.989422 AAAATCCCGTCTTGCTTTCG 57.011 45.000 0.00 0.00 0.00 3.46
2309 2332 0.179137 TGTCTCTCCGTGCTTATGCG 60.179 55.000 0.00 0.00 43.34 4.73
2425 2448 1.989706 TGTGGTTTTGGAGTTAGGCC 58.010 50.000 0.00 0.00 0.00 5.19
2443 2466 1.630148 CCCGCGAAAAGTAGACTGAG 58.370 55.000 8.23 0.00 0.00 3.35
2475 2498 3.840124 AGAGATGCATGCAAGAGATCA 57.160 42.857 26.68 0.00 0.00 2.92
2483 2506 1.081094 TGCAAGAGATCATGTGTGCG 58.919 50.000 0.00 0.00 34.73 5.34
2529 2566 4.142816 CCGCACATTTATTATGCTAGAGCC 60.143 45.833 0.00 0.00 41.18 4.70
2577 2615 2.942804 TCTGGCATTTGACAAGTTGGA 58.057 42.857 7.96 0.00 29.15 3.53
2618 2660 1.303643 GGGCAAACCAGTCAGGGAG 60.304 63.158 0.00 0.00 43.89 4.30
2641 2683 3.991051 CCGCTCGTCCAGGTGTGT 61.991 66.667 0.00 0.00 0.00 3.72
2642 2684 2.734723 CGCTCGTCCAGGTGTGTG 60.735 66.667 0.00 0.00 0.00 3.82
2713 2755 2.404265 TTGCAGAACACAAAGATGCG 57.596 45.000 0.00 0.00 39.74 4.73
2744 2786 0.814010 GCTGTCTTTGACGTGTGGGT 60.814 55.000 0.00 0.00 34.95 4.51
2890 2932 7.282224 GGTTCAGTAGATAATGTGCCATTTACA 59.718 37.037 5.85 0.00 0.00 2.41
2899 2941 3.826524 TGTGCCATTTACAAAGAGGTCA 58.173 40.909 0.00 0.00 0.00 4.02
2911 2953 6.174720 ACAAAGAGGTCATTGAAGACACTA 57.825 37.500 2.12 0.00 40.29 2.74
3034 3150 0.259065 AGTGGATGAGGAGAGCCGTA 59.741 55.000 0.00 0.00 39.96 4.02
3114 3230 8.243426 GGAGATGCAATAACTTTTGATACAACA 58.757 33.333 0.00 0.00 0.00 3.33
3292 3408 2.098607 CACCCGCAGACGATTCTTACTA 59.901 50.000 0.00 0.00 43.93 1.82
3342 3458 6.437928 TCTTGACTTGTTGCATATTGTTGAC 58.562 36.000 0.00 0.00 0.00 3.18
3373 3489 3.664107 AGATGTGTTGAGCGTAATGTGT 58.336 40.909 0.00 0.00 0.00 3.72
3375 3491 2.827652 TGTGTTGAGCGTAATGTGTGA 58.172 42.857 0.00 0.00 0.00 3.58
3425 3564 1.516110 ATGGAGCTGGCTATTGAGGT 58.484 50.000 0.00 0.00 0.00 3.85
3479 3618 1.404035 GTGGCACGTTTTGAAGAAGGT 59.596 47.619 0.00 0.00 0.00 3.50
3575 3714 5.651139 ACATGATCACAGAGGAAGAATTTGG 59.349 40.000 0.00 0.00 0.00 3.28
3636 3775 0.035152 AGCATCCATTCCTGACGCAA 60.035 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.448161 TGTTCCAGTACTCAATCATGATTTGTT 59.552 33.333 18.41 7.78 34.37 2.83
1 2 6.942005 TGTTCCAGTACTCAATCATGATTTGT 59.058 34.615 18.41 19.84 34.37 2.83
2 3 7.381766 TGTTCCAGTACTCAATCATGATTTG 57.618 36.000 18.41 15.58 34.37 2.32
3 4 8.299570 GTTTGTTCCAGTACTCAATCATGATTT 58.700 33.333 18.41 7.24 34.37 2.17
4 5 7.667219 AGTTTGTTCCAGTACTCAATCATGATT 59.333 33.333 15.36 15.36 34.37 2.57
5 6 7.170965 AGTTTGTTCCAGTACTCAATCATGAT 58.829 34.615 1.18 1.18 34.37 2.45
6 7 6.533730 AGTTTGTTCCAGTACTCAATCATGA 58.466 36.000 0.00 0.00 0.00 3.07
7 8 6.652481 AGAGTTTGTTCCAGTACTCAATCATG 59.348 38.462 0.00 0.00 39.51 3.07
8 9 6.773638 AGAGTTTGTTCCAGTACTCAATCAT 58.226 36.000 0.00 0.00 39.51 2.45
9 10 6.174720 AGAGTTTGTTCCAGTACTCAATCA 57.825 37.500 0.00 0.00 39.51 2.57
10 11 8.603242 TTAAGAGTTTGTTCCAGTACTCAATC 57.397 34.615 0.00 0.00 39.51 2.67
11 12 8.211629 ACTTAAGAGTTTGTTCCAGTACTCAAT 58.788 33.333 10.09 0.00 39.51 2.57
12 13 7.562135 ACTTAAGAGTTTGTTCCAGTACTCAA 58.438 34.615 10.09 0.00 39.51 3.02
13 14 7.120923 ACTTAAGAGTTTGTTCCAGTACTCA 57.879 36.000 10.09 0.00 39.51 3.41
14 15 9.538508 TTTACTTAAGAGTTTGTTCCAGTACTC 57.461 33.333 10.09 0.00 37.33 2.59
64 65 9.771534 GCTTCTCCATTAGTCACTCTAATATTT 57.228 33.333 0.00 0.00 44.61 1.40
65 66 8.928448 TGCTTCTCCATTAGTCACTCTAATATT 58.072 33.333 0.00 0.00 44.61 1.28
66 67 8.484214 TGCTTCTCCATTAGTCACTCTAATAT 57.516 34.615 0.00 0.00 44.61 1.28
67 68 7.780271 TCTGCTTCTCCATTAGTCACTCTAATA 59.220 37.037 0.00 0.00 44.61 0.98
68 69 6.609212 TCTGCTTCTCCATTAGTCACTCTAAT 59.391 38.462 0.00 0.00 46.56 1.73
69 70 5.952347 TCTGCTTCTCCATTAGTCACTCTAA 59.048 40.000 0.00 0.00 41.98 2.10
70 71 5.510430 TCTGCTTCTCCATTAGTCACTCTA 58.490 41.667 0.00 0.00 0.00 2.43
71 72 4.348486 TCTGCTTCTCCATTAGTCACTCT 58.652 43.478 0.00 0.00 0.00 3.24
72 73 4.441356 CCTCTGCTTCTCCATTAGTCACTC 60.441 50.000 0.00 0.00 0.00 3.51
73 74 3.450457 CCTCTGCTTCTCCATTAGTCACT 59.550 47.826 0.00 0.00 0.00 3.41
74 75 3.449018 TCCTCTGCTTCTCCATTAGTCAC 59.551 47.826 0.00 0.00 0.00 3.67
75 76 3.703556 CTCCTCTGCTTCTCCATTAGTCA 59.296 47.826 0.00 0.00 0.00 3.41
76 77 3.704061 ACTCCTCTGCTTCTCCATTAGTC 59.296 47.826 0.00 0.00 0.00 2.59
77 78 3.718723 ACTCCTCTGCTTCTCCATTAGT 58.281 45.455 0.00 0.00 0.00 2.24
78 79 5.221422 CCTTACTCCTCTGCTTCTCCATTAG 60.221 48.000 0.00 0.00 0.00 1.73
79 80 4.651503 CCTTACTCCTCTGCTTCTCCATTA 59.348 45.833 0.00 0.00 0.00 1.90
80 81 3.454082 CCTTACTCCTCTGCTTCTCCATT 59.546 47.826 0.00 0.00 0.00 3.16
81 82 3.037549 CCTTACTCCTCTGCTTCTCCAT 58.962 50.000 0.00 0.00 0.00 3.41
82 83 2.225394 ACCTTACTCCTCTGCTTCTCCA 60.225 50.000 0.00 0.00 0.00 3.86
83 84 2.167487 CACCTTACTCCTCTGCTTCTCC 59.833 54.545 0.00 0.00 0.00 3.71
84 85 2.829120 ACACCTTACTCCTCTGCTTCTC 59.171 50.000 0.00 0.00 0.00 2.87
85 86 2.896039 ACACCTTACTCCTCTGCTTCT 58.104 47.619 0.00 0.00 0.00 2.85
86 87 3.259625 AGAACACCTTACTCCTCTGCTTC 59.740 47.826 0.00 0.00 0.00 3.86
87 88 3.243724 AGAACACCTTACTCCTCTGCTT 58.756 45.455 0.00 0.00 0.00 3.91
88 89 2.829120 GAGAACACCTTACTCCTCTGCT 59.171 50.000 0.00 0.00 0.00 4.24
89 90 2.563179 TGAGAACACCTTACTCCTCTGC 59.437 50.000 0.00 0.00 0.00 4.26
90 91 3.194542 CCTGAGAACACCTTACTCCTCTG 59.805 52.174 0.00 0.00 0.00 3.35
91 92 3.436243 CCTGAGAACACCTTACTCCTCT 58.564 50.000 0.00 0.00 0.00 3.69
92 93 2.498078 CCCTGAGAACACCTTACTCCTC 59.502 54.545 0.00 0.00 0.00 3.71
93 94 2.111972 TCCCTGAGAACACCTTACTCCT 59.888 50.000 0.00 0.00 0.00 3.69
94 95 2.498078 CTCCCTGAGAACACCTTACTCC 59.502 54.545 0.00 0.00 0.00 3.85
95 96 3.166679 ACTCCCTGAGAACACCTTACTC 58.833 50.000 0.00 0.00 33.32 2.59
96 97 3.261818 ACTCCCTGAGAACACCTTACT 57.738 47.619 0.00 0.00 33.32 2.24
97 98 4.065789 CAAACTCCCTGAGAACACCTTAC 58.934 47.826 0.00 0.00 33.32 2.34
98 99 3.072476 CCAAACTCCCTGAGAACACCTTA 59.928 47.826 0.00 0.00 33.32 2.69
99 100 2.158608 CCAAACTCCCTGAGAACACCTT 60.159 50.000 0.00 0.00 33.32 3.50
100 101 1.421646 CCAAACTCCCTGAGAACACCT 59.578 52.381 0.00 0.00 33.32 4.00
101 102 1.420138 TCCAAACTCCCTGAGAACACC 59.580 52.381 0.00 0.00 33.32 4.16
102 103 2.930826 TCCAAACTCCCTGAGAACAC 57.069 50.000 0.00 0.00 33.32 3.32
103 104 3.244911 GGATTCCAAACTCCCTGAGAACA 60.245 47.826 0.00 0.00 33.32 3.18
104 105 3.348119 GGATTCCAAACTCCCTGAGAAC 58.652 50.000 0.00 0.00 33.32 3.01
105 106 2.308866 GGGATTCCAAACTCCCTGAGAA 59.691 50.000 4.80 0.00 46.55 2.87
106 107 1.916181 GGGATTCCAAACTCCCTGAGA 59.084 52.381 4.80 0.00 46.55 3.27
107 108 2.426842 GGGATTCCAAACTCCCTGAG 57.573 55.000 4.80 0.00 46.55 3.35
119 120 5.241728 GCTAGAAACATACAATGGGGATTCC 59.758 44.000 0.00 0.00 33.60 3.01
120 121 5.827797 TGCTAGAAACATACAATGGGGATTC 59.172 40.000 0.00 0.00 33.60 2.52
121 122 5.594317 GTGCTAGAAACATACAATGGGGATT 59.406 40.000 0.00 0.00 33.60 3.01
122 123 5.133221 GTGCTAGAAACATACAATGGGGAT 58.867 41.667 0.00 0.00 33.60 3.85
123 124 4.018870 TGTGCTAGAAACATACAATGGGGA 60.019 41.667 0.00 0.00 33.60 4.81
124 125 4.096382 GTGTGCTAGAAACATACAATGGGG 59.904 45.833 0.00 0.00 33.60 4.96
125 126 4.096382 GGTGTGCTAGAAACATACAATGGG 59.904 45.833 0.00 0.00 31.42 4.00
126 127 4.943705 AGGTGTGCTAGAAACATACAATGG 59.056 41.667 0.00 0.00 31.42 3.16
127 128 7.280876 ACATAGGTGTGCTAGAAACATACAATG 59.719 37.037 0.00 2.20 37.14 2.82
128 129 7.338710 ACATAGGTGTGCTAGAAACATACAAT 58.661 34.615 0.00 0.00 37.14 2.71
129 130 6.707290 ACATAGGTGTGCTAGAAACATACAA 58.293 36.000 0.00 0.00 37.14 2.41
130 131 6.294361 ACATAGGTGTGCTAGAAACATACA 57.706 37.500 0.00 0.00 37.14 2.29
131 132 9.627395 CTATACATAGGTGTGCTAGAAACATAC 57.373 37.037 0.00 0.00 39.39 2.39
132 133 9.363401 ACTATACATAGGTGTGCTAGAAACATA 57.637 33.333 0.00 0.00 39.39 2.29
133 134 8.251383 ACTATACATAGGTGTGCTAGAAACAT 57.749 34.615 0.00 0.00 39.39 2.71
134 135 7.340999 TGACTATACATAGGTGTGCTAGAAACA 59.659 37.037 0.00 0.00 39.39 2.83
135 136 7.713750 TGACTATACATAGGTGTGCTAGAAAC 58.286 38.462 0.00 0.00 39.39 2.78
136 137 7.891498 TGACTATACATAGGTGTGCTAGAAA 57.109 36.000 0.00 0.00 39.39 2.52
137 138 9.232473 CTATGACTATACATAGGTGTGCTAGAA 57.768 37.037 0.00 0.00 43.22 2.10
138 139 8.794335 CTATGACTATACATAGGTGTGCTAGA 57.206 38.462 0.00 0.00 43.22 2.43
150 151 9.463902 GTACCACTCCATACTATGACTATACAT 57.536 37.037 0.00 0.00 0.00 2.29
151 152 8.666821 AGTACCACTCCATACTATGACTATACA 58.333 37.037 0.00 0.00 29.70 2.29
152 153 9.517868 AAGTACCACTCCATACTATGACTATAC 57.482 37.037 0.00 0.00 31.30 1.47
153 154 9.516546 CAAGTACCACTCCATACTATGACTATA 57.483 37.037 0.00 0.00 31.30 1.31
154 155 7.451877 CCAAGTACCACTCCATACTATGACTAT 59.548 40.741 0.00 0.00 31.30 2.12
155 156 6.776116 CCAAGTACCACTCCATACTATGACTA 59.224 42.308 0.00 0.00 31.30 2.59
156 157 5.598830 CCAAGTACCACTCCATACTATGACT 59.401 44.000 0.00 0.00 31.30 3.41
157 158 5.597182 TCCAAGTACCACTCCATACTATGAC 59.403 44.000 0.00 0.00 31.30 3.06
158 159 5.773091 TCCAAGTACCACTCCATACTATGA 58.227 41.667 0.00 0.00 31.30 2.15
159 160 5.598830 ACTCCAAGTACCACTCCATACTATG 59.401 44.000 0.00 0.00 31.30 2.23
160 161 5.598830 CACTCCAAGTACCACTCCATACTAT 59.401 44.000 0.00 0.00 31.30 2.12
161 162 4.954202 CACTCCAAGTACCACTCCATACTA 59.046 45.833 0.00 0.00 31.30 1.82
162 163 3.769844 CACTCCAAGTACCACTCCATACT 59.230 47.826 0.00 0.00 32.93 2.12
163 164 3.679083 GCACTCCAAGTACCACTCCATAC 60.679 52.174 0.00 0.00 0.00 2.39
164 165 2.500098 GCACTCCAAGTACCACTCCATA 59.500 50.000 0.00 0.00 0.00 2.74
165 166 1.279271 GCACTCCAAGTACCACTCCAT 59.721 52.381 0.00 0.00 0.00 3.41
166 167 0.685097 GCACTCCAAGTACCACTCCA 59.315 55.000 0.00 0.00 0.00 3.86
167 168 0.389948 CGCACTCCAAGTACCACTCC 60.390 60.000 0.00 0.00 0.00 3.85
168 169 0.601558 TCGCACTCCAAGTACCACTC 59.398 55.000 0.00 0.00 0.00 3.51
169 170 1.045407 TTCGCACTCCAAGTACCACT 58.955 50.000 0.00 0.00 0.00 4.00
170 171 2.094762 ATTCGCACTCCAAGTACCAC 57.905 50.000 0.00 0.00 0.00 4.16
171 172 2.851263 AATTCGCACTCCAAGTACCA 57.149 45.000 0.00 0.00 0.00 3.25
172 173 3.500680 TGAAAATTCGCACTCCAAGTACC 59.499 43.478 0.00 0.00 0.00 3.34
173 174 4.712763 CTGAAAATTCGCACTCCAAGTAC 58.287 43.478 0.00 0.00 0.00 2.73
174 175 3.188460 GCTGAAAATTCGCACTCCAAGTA 59.812 43.478 5.52 0.00 0.00 2.24
175 176 2.030805 GCTGAAAATTCGCACTCCAAGT 60.031 45.455 5.52 0.00 0.00 3.16
176 177 2.589014 GCTGAAAATTCGCACTCCAAG 58.411 47.619 5.52 0.00 0.00 3.61
215 216 0.381089 AAGAACGACGAGGATAGCGG 59.619 55.000 0.00 0.00 0.00 5.52
270 271 2.295349 CGTATTCCTTTCGCTAGGCCTA 59.705 50.000 13.09 13.09 35.15 3.93
292 293 2.203596 CCTAGGCGTATCCCGGGT 60.204 66.667 22.86 10.79 36.94 5.28
310 311 3.063588 GCACAGAATACGCCTACCTTTTC 59.936 47.826 0.00 0.00 0.00 2.29
350 351 4.263572 CCAGCGTGTGGGGGACAA 62.264 66.667 0.00 0.00 43.63 3.18
403 404 4.442052 CCTCGAGGATTCTGTGCTATTTCA 60.442 45.833 28.21 0.00 37.39 2.69
523 531 2.589540 GATGGATGGGTGTCGGCA 59.410 61.111 0.00 0.00 0.00 5.69
529 537 0.403271 GAGATGGGGATGGATGGGTG 59.597 60.000 0.00 0.00 0.00 4.61
563 577 4.664677 AGCACAGTCACCGCGGTC 62.665 66.667 31.80 19.35 0.00 4.79
594 608 1.228228 GCAGATGGGGATGGAGCAA 59.772 57.895 0.00 0.00 0.00 3.91
608 622 0.895100 GTGCCCCAAACAGATGCAGA 60.895 55.000 0.00 0.00 31.69 4.26
647 661 4.037565 ACGGCAATCAAGTAGATATCACGA 59.962 41.667 5.32 0.00 35.39 4.35
650 664 5.279006 GGAGACGGCAATCAAGTAGATATCA 60.279 44.000 5.32 0.00 35.39 2.15
666 680 2.750888 GCAAACGGATGGAGACGGC 61.751 63.158 0.00 0.00 0.00 5.68
687 701 0.107410 TGTGCTGTGAAAGACCCGTT 60.107 50.000 0.00 0.00 0.00 4.44
753 771 1.355381 AGAAACATGATGCAGGGACCA 59.645 47.619 0.00 0.00 0.00 4.02
773 791 5.006844 TGAAGAACACGCGACAGAAAATTAA 59.993 36.000 15.93 0.00 0.00 1.40
774 792 4.508492 TGAAGAACACGCGACAGAAAATTA 59.492 37.500 15.93 0.00 0.00 1.40
775 793 3.311322 TGAAGAACACGCGACAGAAAATT 59.689 39.130 15.93 0.00 0.00 1.82
776 794 2.869801 TGAAGAACACGCGACAGAAAAT 59.130 40.909 15.93 0.00 0.00 1.82
784 802 3.026630 AGAAATCTGAAGAACACGCGA 57.973 42.857 15.93 0.00 0.00 5.87
819 837 6.150641 AGCACACATCCTATATGAATGCAATC 59.849 38.462 15.39 0.00 36.56 2.67
820 838 6.008331 AGCACACATCCTATATGAATGCAAT 58.992 36.000 15.39 0.00 36.56 3.56
821 839 5.379187 AGCACACATCCTATATGAATGCAA 58.621 37.500 15.39 0.00 36.56 4.08
823 841 5.390251 CGAAGCACACATCCTATATGAATGC 60.390 44.000 8.95 8.95 35.36 3.56
824 842 6.161911 CGAAGCACACATCCTATATGAATG 57.838 41.667 0.00 0.00 0.00 2.67
879 897 3.492309 GCTCATCGAATCCTGTGACTCAT 60.492 47.826 0.00 0.00 0.00 2.90
886 904 0.103208 GGACGCTCATCGAATCCTGT 59.897 55.000 0.00 0.00 41.67 4.00
936 955 2.280457 GCATCCCCGACTAGCTGC 60.280 66.667 0.00 0.00 0.00 5.25
986 1005 2.352422 ACATGCGTGTCCAGCCAT 59.648 55.556 5.51 0.00 31.41 4.40
1001 1020 5.581126 AACAGAGCAATTTTTCACTGACA 57.419 34.783 0.00 0.00 0.00 3.58
1005 1024 5.876460 AGCAAAAACAGAGCAATTTTTCACT 59.124 32.000 0.00 0.00 36.18 3.41
1017 1036 1.335810 TGCAGCAGAGCAAAAACAGAG 59.664 47.619 0.00 0.00 42.46 3.35
1105 1124 7.171678 CCCAACAAAAACAACACACTTCTTAAA 59.828 33.333 0.00 0.00 0.00 1.52
1111 1130 4.344359 ACCCAACAAAAACAACACACTT 57.656 36.364 0.00 0.00 0.00 3.16
1125 1144 4.039004 CAGATCATCAAACCAAACCCAACA 59.961 41.667 0.00 0.00 0.00 3.33
1131 1150 5.320549 AGCATCAGATCATCAAACCAAAC 57.679 39.130 0.00 0.00 0.00 2.93
1139 1158 5.247792 ACCTAATGCTAGCATCAGATCATCA 59.752 40.000 29.67 6.69 35.31 3.07
1142 1161 5.777223 ACTACCTAATGCTAGCATCAGATCA 59.223 40.000 29.67 12.20 35.31 2.92
1179 1198 7.864882 TCAATAAAATCGAACAAACTGCATCAA 59.135 29.630 0.00 0.00 0.00 2.57
1180 1199 7.366513 TCAATAAAATCGAACAAACTGCATCA 58.633 30.769 0.00 0.00 0.00 3.07
1185 1204 9.778993 AGATCATCAATAAAATCGAACAAACTG 57.221 29.630 0.00 0.00 0.00 3.16
1195 1214 8.929746 TGCTACGATCAGATCATCAATAAAATC 58.070 33.333 11.12 0.00 0.00 2.17
1215 1234 5.345702 TGCAGTTTACTACCTAATGCTACG 58.654 41.667 0.00 0.00 33.47 3.51
1222 1241 5.556006 ACCAGTTGCAGTTTACTACCTAA 57.444 39.130 0.00 0.00 0.00 2.69
1278 1297 7.182817 TCTGTGTTTCACTACCTAATGCTAT 57.817 36.000 1.72 0.00 35.11 2.97
1324 1343 5.532406 ACAACATAAGTCACTGCAACTGAAT 59.468 36.000 0.00 0.00 0.00 2.57
1413 1432 4.540099 AGAAATCCAAGACCATCACCCTAA 59.460 41.667 0.00 0.00 0.00 2.69
1414 1433 4.111577 AGAAATCCAAGACCATCACCCTA 58.888 43.478 0.00 0.00 0.00 3.53
1443 1462 6.488683 CCCACAAAACTCCAATGTACTCTAAA 59.511 38.462 0.00 0.00 0.00 1.85
1445 1464 5.072600 ACCCACAAAACTCCAATGTACTCTA 59.927 40.000 0.00 0.00 0.00 2.43
1447 1466 4.142038 ACCCACAAAACTCCAATGTACTC 58.858 43.478 0.00 0.00 0.00 2.59
1450 1469 4.461081 GCATACCCACAAAACTCCAATGTA 59.539 41.667 0.00 0.00 0.00 2.29
1470 1489 4.081531 CCCACACACCAATCTAAAATGCAT 60.082 41.667 0.00 0.00 0.00 3.96
1475 1494 2.950781 TGCCCACACACCAATCTAAAA 58.049 42.857 0.00 0.00 0.00 1.52
1520 1539 5.302823 GCTAATCCAACAAGCCATCCTAAAT 59.697 40.000 0.00 0.00 0.00 1.40
1535 1554 2.487762 CGGTCAAGCTTTGCTAATCCAA 59.512 45.455 0.00 0.00 38.25 3.53
1538 1557 1.529826 CGCGGTCAAGCTTTGCTAATC 60.530 52.381 0.00 0.00 38.25 1.75
1547 1566 4.070552 GTCCTCCGCGGTCAAGCT 62.071 66.667 27.15 0.00 34.40 3.74
1567 1586 5.644644 CAAATGAAGATACCCAACAAGCTC 58.355 41.667 0.00 0.00 0.00 4.09
1613 1633 8.794335 AACTCCCTAATACAACTTTTCATCTC 57.206 34.615 0.00 0.00 0.00 2.75
1632 1652 8.496707 TTTTCTTACATCCGTATTAAACTCCC 57.503 34.615 0.00 0.00 0.00 4.30
1651 1671 6.879458 ACCTCATTATCACTAACGCTTTTCTT 59.121 34.615 0.00 0.00 0.00 2.52
1654 1674 9.998106 ATATACCTCATTATCACTAACGCTTTT 57.002 29.630 0.00 0.00 0.00 2.27
1655 1675 9.998106 AATATACCTCATTATCACTAACGCTTT 57.002 29.630 0.00 0.00 0.00 3.51
1670 1690 7.183475 ACCTTCTGCCATCATAATATACCTCAT 59.817 37.037 0.00 0.00 0.00 2.90
1671 1691 6.501805 ACCTTCTGCCATCATAATATACCTCA 59.498 38.462 0.00 0.00 0.00 3.86
1673 1693 6.959606 ACCTTCTGCCATCATAATATACCT 57.040 37.500 0.00 0.00 0.00 3.08
1674 1694 6.375455 CCAACCTTCTGCCATCATAATATACC 59.625 42.308 0.00 0.00 0.00 2.73
1675 1695 6.942576 ACCAACCTTCTGCCATCATAATATAC 59.057 38.462 0.00 0.00 0.00 1.47
1676 1696 6.942005 CACCAACCTTCTGCCATCATAATATA 59.058 38.462 0.00 0.00 0.00 0.86
1677 1697 5.771666 CACCAACCTTCTGCCATCATAATAT 59.228 40.000 0.00 0.00 0.00 1.28
1678 1698 5.132502 CACCAACCTTCTGCCATCATAATA 58.867 41.667 0.00 0.00 0.00 0.98
1679 1699 3.956199 CACCAACCTTCTGCCATCATAAT 59.044 43.478 0.00 0.00 0.00 1.28
1680 1700 3.245229 ACACCAACCTTCTGCCATCATAA 60.245 43.478 0.00 0.00 0.00 1.90
1681 1701 2.308570 ACACCAACCTTCTGCCATCATA 59.691 45.455 0.00 0.00 0.00 2.15
1682 1702 1.076024 ACACCAACCTTCTGCCATCAT 59.924 47.619 0.00 0.00 0.00 2.45
1683 1703 0.478072 ACACCAACCTTCTGCCATCA 59.522 50.000 0.00 0.00 0.00 3.07
1684 1704 0.883833 CACACCAACCTTCTGCCATC 59.116 55.000 0.00 0.00 0.00 3.51
1685 1705 0.185901 ACACACCAACCTTCTGCCAT 59.814 50.000 0.00 0.00 0.00 4.40
1686 1706 0.033601 AACACACCAACCTTCTGCCA 60.034 50.000 0.00 0.00 0.00 4.92
1687 1707 0.385390 CAACACACCAACCTTCTGCC 59.615 55.000 0.00 0.00 0.00 4.85
1688 1708 0.385390 CCAACACACCAACCTTCTGC 59.615 55.000 0.00 0.00 0.00 4.26
1689 1709 2.051334 TCCAACACACCAACCTTCTG 57.949 50.000 0.00 0.00 0.00 3.02
1690 1710 3.312736 AATCCAACACACCAACCTTCT 57.687 42.857 0.00 0.00 0.00 2.85
1691 1711 3.636764 AGAAATCCAACACACCAACCTTC 59.363 43.478 0.00 0.00 0.00 3.46
1692 1712 3.642141 AGAAATCCAACACACCAACCTT 58.358 40.909 0.00 0.00 0.00 3.50
1693 1713 3.312736 AGAAATCCAACACACCAACCT 57.687 42.857 0.00 0.00 0.00 3.50
1694 1714 4.142038 ACTAGAAATCCAACACACCAACC 58.858 43.478 0.00 0.00 0.00 3.77
1695 1715 5.767816 AACTAGAAATCCAACACACCAAC 57.232 39.130 0.00 0.00 0.00 3.77
1696 1716 5.451242 GCAAACTAGAAATCCAACACACCAA 60.451 40.000 0.00 0.00 0.00 3.67
1697 1717 4.037446 GCAAACTAGAAATCCAACACACCA 59.963 41.667 0.00 0.00 0.00 4.17
1698 1718 4.278419 AGCAAACTAGAAATCCAACACACC 59.722 41.667 0.00 0.00 0.00 4.16
1699 1719 5.008613 TCAGCAAACTAGAAATCCAACACAC 59.991 40.000 0.00 0.00 0.00 3.82
1700 1720 5.129634 TCAGCAAACTAGAAATCCAACACA 58.870 37.500 0.00 0.00 0.00 3.72
1701 1721 5.689383 TCAGCAAACTAGAAATCCAACAC 57.311 39.130 0.00 0.00 0.00 3.32
1702 1722 6.294675 CCAATCAGCAAACTAGAAATCCAACA 60.295 38.462 0.00 0.00 0.00 3.33
1709 1729 6.959639 AGTTTCCAATCAGCAAACTAGAAA 57.040 33.333 0.00 0.00 36.47 2.52
1756 1776 2.669781 CCAATGCCCATACACCAATCT 58.330 47.619 0.00 0.00 0.00 2.40
1802 1822 1.202348 CCAGGCGACAAAAATTCCTCC 59.798 52.381 0.00 0.00 0.00 4.30
1841 1861 8.107399 TCGATCGTAATCAATAACACTATCCT 57.893 34.615 15.94 0.00 31.76 3.24
1842 1862 8.912787 ATCGATCGTAATCAATAACACTATCC 57.087 34.615 15.94 0.00 31.76 2.59
1893 1913 6.313252 TCAAGAAATGTTTTTGCAGCAAAAC 58.687 32.000 29.13 23.02 42.02 2.43
1939 1959 4.159321 ACACACATCACAAACAATCCAACA 59.841 37.500 0.00 0.00 0.00 3.33
1954 1974 6.238211 GCCATTGACTATACTCAACACACATC 60.238 42.308 0.00 0.00 32.95 3.06
1975 1995 0.975887 AAAAACAATCGGCCAGCCAT 59.024 45.000 9.78 0.00 35.37 4.40
1980 2000 3.491104 GGTGTTGTAAAAACAATCGGCCA 60.491 43.478 2.24 0.00 35.09 5.36
1983 2003 5.583495 TGAAGGTGTTGTAAAAACAATCGG 58.417 37.500 0.00 0.00 35.09 4.18
1988 2008 4.096532 TCGCATGAAGGTGTTGTAAAAACA 59.903 37.500 0.00 0.00 35.09 2.83
2015 2035 4.439563 CCCTTACATAAATTTGTGGCGACC 60.440 45.833 17.83 0.00 0.00 4.79
2042 2062 5.472137 ACGTAACAACCAATTACAGCATCTT 59.528 36.000 0.00 0.00 32.98 2.40
2065 2085 9.953697 TTTGCAATTACATAATTAACCGGATAC 57.046 29.630 9.46 0.00 34.36 2.24
2092 2112 5.642063 CACCATACAGTTTAAAGACCATCGT 59.358 40.000 0.00 0.00 0.00 3.73
2094 2114 6.879458 ACTCACCATACAGTTTAAAGACCATC 59.121 38.462 0.00 0.00 0.00 3.51
2099 2119 6.481976 CACACACTCACCATACAGTTTAAAGA 59.518 38.462 0.00 0.00 0.00 2.52
2127 2147 4.340950 ACGGGATTTTTCATGTTCACAGTT 59.659 37.500 0.00 0.00 0.00 3.16
2128 2148 3.888930 ACGGGATTTTTCATGTTCACAGT 59.111 39.130 0.00 0.00 0.00 3.55
2148 2169 0.042188 CACACACCGAAAGCAAGACG 60.042 55.000 0.00 0.00 0.00 4.18
2160 2181 4.156455 ACCATTAGATCATCCACACACC 57.844 45.455 0.00 0.00 0.00 4.16
2309 2332 1.777272 ACAGGGCCATCCTTCTTATCC 59.223 52.381 6.18 0.00 45.47 2.59
2425 2448 1.986378 CACTCAGTCTACTTTTCGCGG 59.014 52.381 6.13 0.00 0.00 6.46
2443 2466 1.067565 TGCATCTCTTCCTGTCGACAC 60.068 52.381 15.76 1.03 0.00 3.67
2450 2473 2.614520 CTCTTGCATGCATCTCTTCCTG 59.385 50.000 23.37 3.86 0.00 3.86
2475 2498 1.155889 CATACCACACACGCACACAT 58.844 50.000 0.00 0.00 0.00 3.21
2483 2506 4.093850 GGTTCCGAATTACATACCACACAC 59.906 45.833 0.00 0.00 0.00 3.82
2529 2566 8.437360 TCATACTCATTGCACCTTAACATAAG 57.563 34.615 0.00 0.00 0.00 1.73
2610 2652 2.435059 GCGGCTGTTCTCCCTGAC 60.435 66.667 0.00 0.00 0.00 3.51
2618 2660 2.811317 CTGGACGAGCGGCTGTTC 60.811 66.667 7.50 5.56 0.00 3.18
2665 2707 5.278463 CCACCCTTTGTCATTTGACTACAAG 60.278 44.000 11.67 10.22 44.99 3.16
2669 2711 4.447138 ACCACCCTTTGTCATTTGACTA 57.553 40.909 11.67 1.70 44.99 2.59
2670 2712 3.312736 ACCACCCTTTGTCATTTGACT 57.687 42.857 11.67 0.00 44.99 3.41
2713 2755 1.668419 AAGACAGCGGGTGATTATGC 58.332 50.000 14.98 0.00 0.00 3.14
2744 2786 2.232452 GAGACTTCCAGTGCAGCTTCTA 59.768 50.000 0.00 0.00 0.00 2.10
2890 2932 6.773638 ACATAGTGTCTTCAATGACCTCTTT 58.226 36.000 0.00 0.00 36.21 2.52
2899 2941 9.654663 GTTAGTTTCCTACATAGTGTCTTCAAT 57.345 33.333 0.00 0.00 0.00 2.57
2911 2953 8.110908 AGACTACTCTCTGTTAGTTTCCTACAT 58.889 37.037 0.00 0.00 0.00 2.29
3034 3150 7.589958 TTGTTACCCACATCAGTGTTTTTAT 57.410 32.000 0.00 0.00 44.39 1.40
3114 3230 8.585881 GGCATATCATATAGATTGGTACGGTAT 58.414 37.037 0.00 0.00 38.19 2.73
3190 3306 1.750018 CCCTCATCATTGCGCCACA 60.750 57.895 4.18 0.00 0.00 4.17
3292 3408 6.513393 GCAGCACAGTTCATTTGTTACTAACT 60.513 38.462 0.71 0.00 0.00 2.24
3359 3475 7.589395 ACATTTTAATCACACATTACGCTCAA 58.411 30.769 0.00 0.00 0.00 3.02
3364 3480 9.283420 TGCATTACATTTTAATCACACATTACG 57.717 29.630 0.00 0.00 0.00 3.18
3373 3489 7.428020 GCCTGATCTGCATTACATTTTAATCA 58.572 34.615 0.00 0.00 0.00 2.57
3375 3491 6.441274 CGCCTGATCTGCATTACATTTTAAT 58.559 36.000 8.24 0.00 0.00 1.40
3425 3564 5.507817 CGGTGTACTGTGTTTGGTAGTTCTA 60.508 44.000 0.00 0.00 0.00 2.10
3479 3618 0.608130 CACACCCATCGACTCCTTCA 59.392 55.000 0.00 0.00 0.00 3.02
3575 3714 1.001641 ATGTCCTGCCAACCAGCTC 60.002 57.895 0.00 0.00 40.36 4.09


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

AutoCloner maintained by Alex Coulton.