Multiple sequence alignment - TraesCS6D01G052100

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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 TraesCS6D01G052100 chr6D 100.000 5467 0 0 1 5467 24833436 24827970 0.000000e+00 10096.0
1 TraesCS6D01G052100 chr6D 94.382 89 5 0 78 166 155146868 155146780 2.660000e-28 137.0
2 TraesCS6D01G052100 chr6B 91.302 4369 233 65 211 4491 40448915 40453224 0.000000e+00 5827.0
3 TraesCS6D01G052100 chr6B 88.265 588 61 7 4814 5396 713473920 713474504 0.000000e+00 697.0
4 TraesCS6D01G052100 chr6B 95.349 86 4 0 83 168 73362 73277 2.660000e-28 137.0
5 TraesCS6D01G052100 chr6A 94.019 3695 153 37 1137 4791 23366420 23362754 0.000000e+00 5537.0
6 TraesCS6D01G052100 chr6A 85.012 407 25 12 178 577 23367376 23366999 1.110000e-101 381.0
7 TraesCS6D01G052100 chr6A 93.023 43 2 1 1 42 23367552 23367510 1.640000e-05 62.1
8 TraesCS6D01G052100 chr2A 87.284 810 71 18 3714 4510 331189181 331189971 0.000000e+00 896.0
9 TraesCS6D01G052100 chr2A 88.820 644 57 10 4788 5422 197486365 197487002 0.000000e+00 776.0
10 TraesCS6D01G052100 chr4A 91.824 636 47 3 4790 5422 690100249 690100882 0.000000e+00 881.0
11 TraesCS6D01G052100 chr4A 83.278 604 53 12 1172 1767 727710189 727710752 3.780000e-141 512.0
12 TraesCS6D01G052100 chr4A 93.548 93 6 0 76 168 668943957 668943865 7.380000e-29 139.0
13 TraesCS6D01G052100 chr3A 86.757 808 81 10 3713 4510 198238235 198239026 0.000000e+00 876.0
14 TraesCS6D01G052100 chr7A 86.313 811 76 18 3713 4510 271498720 271497932 0.000000e+00 850.0
15 TraesCS6D01G052100 chr7A 76.557 610 109 29 3621 4215 628663965 628664555 2.470000e-78 303.0
16 TraesCS6D01G052100 chr7A 95.238 84 4 0 83 166 558288807 558288724 3.440000e-27 134.0
17 TraesCS6D01G052100 chrUn 85.680 845 67 21 211 1049 96632869 96632073 0.000000e+00 841.0
18 TraesCS6D01G052100 chr7B 84.589 876 80 26 211 1079 691414287 691415114 0.000000e+00 819.0
19 TraesCS6D01G052100 chr7B 86.739 641 71 9 4790 5422 384764372 384765006 0.000000e+00 701.0
20 TraesCS6D01G052100 chr7B 85.033 608 66 15 479 1079 558938575 558937986 3.650000e-166 595.0
21 TraesCS6D01G052100 chr7B 90.093 323 22 7 1448 1767 724347954 724347639 1.420000e-110 411.0
22 TraesCS6D01G052100 chr7B 78.354 559 92 25 3621 4166 589961218 589961760 8.770000e-88 335.0
23 TraesCS6D01G052100 chr7B 88.983 118 8 4 1303 1416 724348072 724347956 2.050000e-29 141.0
24 TraesCS6D01G052100 chr7B 80.233 86 13 3 4576 4657 615381194 615381109 1.640000e-05 62.1
25 TraesCS6D01G052100 chr7B 92.308 39 3 0 1478 1516 57679981 57679943 7.650000e-04 56.5
26 TraesCS6D01G052100 chr7B 100.000 28 0 0 3069 3096 588893052 588893025 1.000000e-02 52.8
27 TraesCS6D01G052100 chr4B 84.607 877 74 25 211 1079 350107782 350106959 0.000000e+00 815.0
28 TraesCS6D01G052100 chr4B 84.439 829 82 25 3713 4510 476635019 476634207 0.000000e+00 773.0
29 TraesCS6D01G052100 chr4B 85.671 656 60 14 4790 5421 602210579 602209934 0.000000e+00 660.0
30 TraesCS6D01G052100 chr3B 84.379 877 81 27 214 1079 88472738 88471907 0.000000e+00 809.0
31 TraesCS6D01G052100 chr3B 87.059 595 58 12 458 1049 13892251 13891673 0.000000e+00 654.0
32 TraesCS6D01G052100 chr2D 89.596 644 55 4 4790 5430 611164330 611164964 0.000000e+00 808.0
33 TraesCS6D01G052100 chr2D 88.000 600 63 7 4785 5380 613218222 613218816 0.000000e+00 701.0
34 TraesCS6D01G052100 chr2D 87.220 626 65 8 4802 5421 603660827 603661443 0.000000e+00 699.0
35 TraesCS6D01G052100 chr2D 85.873 630 61 17 458 1079 582683100 582682491 0.000000e+00 645.0
36 TraesCS6D01G052100 chr3D 85.559 644 67 17 4791 5422 525920677 525920048 0.000000e+00 651.0
37 TraesCS6D01G052100 chr3D 86.116 605 54 15 479 1079 31598163 31597585 4.650000e-175 625.0
38 TraesCS6D01G052100 chr3D 91.753 97 6 2 72 166 26781329 26781425 3.440000e-27 134.0
39 TraesCS6D01G052100 chr1B 86.606 545 59 10 542 1079 563375942 563376479 1.700000e-164 590.0
40 TraesCS6D01G052100 chr5B 87.209 516 44 10 1166 1676 51976829 51977327 7.950000e-158 568.0
41 TraesCS6D01G052100 chr5B 94.444 90 5 0 78 167 547268439 547268528 7.380000e-29 139.0
42 TraesCS6D01G052100 chr7D 76.480 608 113 26 3621 4215 545696566 545697156 2.470000e-78 303.0
43 TraesCS6D01G052100 chr7D 100.000 29 0 0 1478 1506 101138561 101138533 3.000000e-03 54.7
44 TraesCS6D01G052100 chr7D 100.000 28 0 0 3069 3096 545301872 545301845 1.000000e-02 52.8
45 TraesCS6D01G052100 chr1A 91.597 119 10 0 1643 1761 14524231 14524113 1.220000e-36 165.0
46 TraesCS6D01G052100 chr2B 95.604 91 4 0 78 168 397449921 397449831 4.410000e-31 147.0
47 TraesCS6D01G052100 chr2B 90.816 98 9 0 70 167 178650014 178649917 1.240000e-26 132.0
48 TraesCS6D01G052100 chr4D 93.548 93 5 1 77 168 71301594 71301686 2.660000e-28 137.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G052100 chr6D 24827970 24833436 5466 True 10096.000000 10096 100.000000 1 5467 1 chr6D.!!$R1 5466
1 TraesCS6D01G052100 chr6B 40448915 40453224 4309 False 5827.000000 5827 91.302000 211 4491 1 chr6B.!!$F1 4280
2 TraesCS6D01G052100 chr6B 713473920 713474504 584 False 697.000000 697 88.265000 4814 5396 1 chr6B.!!$F2 582
3 TraesCS6D01G052100 chr6A 23362754 23367552 4798 True 1993.366667 5537 90.684667 1 4791 3 chr6A.!!$R1 4790
4 TraesCS6D01G052100 chr2A 331189181 331189971 790 False 896.000000 896 87.284000 3714 4510 1 chr2A.!!$F2 796
5 TraesCS6D01G052100 chr2A 197486365 197487002 637 False 776.000000 776 88.820000 4788 5422 1 chr2A.!!$F1 634
6 TraesCS6D01G052100 chr4A 690100249 690100882 633 False 881.000000 881 91.824000 4790 5422 1 chr4A.!!$F1 632
7 TraesCS6D01G052100 chr4A 727710189 727710752 563 False 512.000000 512 83.278000 1172 1767 1 chr4A.!!$F2 595
8 TraesCS6D01G052100 chr3A 198238235 198239026 791 False 876.000000 876 86.757000 3713 4510 1 chr3A.!!$F1 797
9 TraesCS6D01G052100 chr7A 271497932 271498720 788 True 850.000000 850 86.313000 3713 4510 1 chr7A.!!$R1 797
10 TraesCS6D01G052100 chr7A 628663965 628664555 590 False 303.000000 303 76.557000 3621 4215 1 chr7A.!!$F1 594
11 TraesCS6D01G052100 chrUn 96632073 96632869 796 True 841.000000 841 85.680000 211 1049 1 chrUn.!!$R1 838
12 TraesCS6D01G052100 chr7B 691414287 691415114 827 False 819.000000 819 84.589000 211 1079 1 chr7B.!!$F3 868
13 TraesCS6D01G052100 chr7B 384764372 384765006 634 False 701.000000 701 86.739000 4790 5422 1 chr7B.!!$F1 632
14 TraesCS6D01G052100 chr7B 558937986 558938575 589 True 595.000000 595 85.033000 479 1079 1 chr7B.!!$R2 600
15 TraesCS6D01G052100 chr7B 589961218 589961760 542 False 335.000000 335 78.354000 3621 4166 1 chr7B.!!$F2 545
16 TraesCS6D01G052100 chr4B 350106959 350107782 823 True 815.000000 815 84.607000 211 1079 1 chr4B.!!$R1 868
17 TraesCS6D01G052100 chr4B 476634207 476635019 812 True 773.000000 773 84.439000 3713 4510 1 chr4B.!!$R2 797
18 TraesCS6D01G052100 chr4B 602209934 602210579 645 True 660.000000 660 85.671000 4790 5421 1 chr4B.!!$R3 631
19 TraesCS6D01G052100 chr3B 88471907 88472738 831 True 809.000000 809 84.379000 214 1079 1 chr3B.!!$R2 865
20 TraesCS6D01G052100 chr3B 13891673 13892251 578 True 654.000000 654 87.059000 458 1049 1 chr3B.!!$R1 591
21 TraesCS6D01G052100 chr2D 611164330 611164964 634 False 808.000000 808 89.596000 4790 5430 1 chr2D.!!$F2 640
22 TraesCS6D01G052100 chr2D 613218222 613218816 594 False 701.000000 701 88.000000 4785 5380 1 chr2D.!!$F3 595
23 TraesCS6D01G052100 chr2D 603660827 603661443 616 False 699.000000 699 87.220000 4802 5421 1 chr2D.!!$F1 619
24 TraesCS6D01G052100 chr2D 582682491 582683100 609 True 645.000000 645 85.873000 458 1079 1 chr2D.!!$R1 621
25 TraesCS6D01G052100 chr3D 525920048 525920677 629 True 651.000000 651 85.559000 4791 5422 1 chr3D.!!$R2 631
26 TraesCS6D01G052100 chr3D 31597585 31598163 578 True 625.000000 625 86.116000 479 1079 1 chr3D.!!$R1 600
27 TraesCS6D01G052100 chr1B 563375942 563376479 537 False 590.000000 590 86.606000 542 1079 1 chr1B.!!$F1 537
28 TraesCS6D01G052100 chr7D 545696566 545697156 590 False 303.000000 303 76.480000 3621 4215 1 chr7D.!!$F1 594

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
94 174 0.179070 GCTCATTCTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.0 3.62 F
584 686 0.391228 TTGGCTTGCGTACTCAGTCA 59.609 50.000 0.00 0.00 0.0 3.41 F
2451 2689 0.250295 TGCTCACCAAGAACTTCCGG 60.250 55.000 0.00 0.00 0.0 5.14 F
3129 3367 1.214062 CTTCACCTTCTCGAGCGCT 59.786 57.895 11.27 11.27 0.0 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1364 0.657840 ATTTGCAGCTAACGATCGCC 59.342 50.000 16.60 1.05 0.00 5.54 R
2563 2801 1.188219 TCGAGCACCTTGAGCTTCCT 61.188 55.000 0.00 0.00 43.58 3.36 R
3378 3616 1.006571 GGTGCTTTCCTCGTCGTCA 60.007 57.895 0.00 0.00 0.00 4.35 R
5038 5329 0.250727 CCACACCCTTCATTGACGGT 60.251 55.000 8.26 3.94 0.00 4.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 146 7.613022 TCAATAATTCTCACAGGAAATTCAGCT 59.387 33.333 0.00 0.00 0.00 4.24
70 150 2.746362 CTCACAGGAAATTCAGCTGGTC 59.254 50.000 15.13 6.48 0.00 4.02
84 164 1.742268 GCTGGTCCAAAGCTCATTCTC 59.258 52.381 0.00 0.00 37.69 2.87
85 165 2.363683 CTGGTCCAAAGCTCATTCTCC 58.636 52.381 0.00 0.00 0.00 3.71
86 166 1.004745 TGGTCCAAAGCTCATTCTCCC 59.995 52.381 0.00 0.00 0.00 4.30
88 168 2.637947 GTCCAAAGCTCATTCTCCCTC 58.362 52.381 0.00 0.00 0.00 4.30
89 169 1.561542 TCCAAAGCTCATTCTCCCTCC 59.438 52.381 0.00 0.00 0.00 4.30
90 170 1.661341 CAAAGCTCATTCTCCCTCCG 58.339 55.000 0.00 0.00 0.00 4.63
91 171 1.065854 CAAAGCTCATTCTCCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
92 172 1.280457 AAGCTCATTCTCCCTCCGTT 58.720 50.000 0.00 0.00 0.00 4.44
94 174 0.179070 GCTCATTCTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
95 175 1.195115 CTCATTCTCCCTCCGTTCCA 58.805 55.000 0.00 0.00 0.00 3.53
96 176 1.555075 CTCATTCTCCCTCCGTTCCAA 59.445 52.381 0.00 0.00 0.00 3.53
97 177 1.982226 TCATTCTCCCTCCGTTCCAAA 59.018 47.619 0.00 0.00 0.00 3.28
98 178 2.373836 TCATTCTCCCTCCGTTCCAAAA 59.626 45.455 0.00 0.00 0.00 2.44
99 179 3.010138 TCATTCTCCCTCCGTTCCAAAAT 59.990 43.478 0.00 0.00 0.00 1.82
100 180 4.226394 TCATTCTCCCTCCGTTCCAAAATA 59.774 41.667 0.00 0.00 0.00 1.40
101 181 3.906720 TCTCCCTCCGTTCCAAAATAG 57.093 47.619 0.00 0.00 0.00 1.73
102 182 3.446968 TCTCCCTCCGTTCCAAAATAGA 58.553 45.455 0.00 0.00 0.00 1.98
103 183 4.037927 TCTCCCTCCGTTCCAAAATAGAT 58.962 43.478 0.00 0.00 0.00 1.98
104 184 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
105 185 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
106 186 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
107 187 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
108 188 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
109 189 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
110 190 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
111 191 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
112 192 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
113 193 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
114 194 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
115 195 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
116 196 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
117 197 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
118 198 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
119 199 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
120 200 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
121 201 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
122 202 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
123 203 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
124 204 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
125 205 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
126 206 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
127 207 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
128 208 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
129 209 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
142 222 8.482852 ACTAACTTTAGTACAAAGTAGGGTCA 57.517 34.615 17.85 5.36 41.92 4.02
143 223 9.097946 ACTAACTTTAGTACAAAGTAGGGTCAT 57.902 33.333 17.85 8.16 41.92 3.06
144 224 9.583765 CTAACTTTAGTACAAAGTAGGGTCATC 57.416 37.037 17.85 0.00 39.36 2.92
145 225 7.793948 ACTTTAGTACAAAGTAGGGTCATCT 57.206 36.000 16.72 0.00 38.58 2.90
146 226 8.890410 ACTTTAGTACAAAGTAGGGTCATCTA 57.110 34.615 16.72 0.00 38.58 1.98
147 227 9.490083 ACTTTAGTACAAAGTAGGGTCATCTAT 57.510 33.333 16.72 0.00 38.58 1.98
152 232 8.822805 AGTACAAAGTAGGGTCATCTATTTTGA 58.177 33.333 19.37 7.09 43.50 2.69
153 233 9.444600 GTACAAAGTAGGGTCATCTATTTTGAA 57.555 33.333 19.37 0.00 43.50 2.69
154 234 8.934023 ACAAAGTAGGGTCATCTATTTTGAAA 57.066 30.769 19.37 0.00 43.50 2.69
155 235 8.793592 ACAAAGTAGGGTCATCTATTTTGAAAC 58.206 33.333 19.37 0.00 43.50 2.78
156 236 7.939784 AAGTAGGGTCATCTATTTTGAAACC 57.060 36.000 0.00 0.00 0.00 3.27
157 237 7.027874 AGTAGGGTCATCTATTTTGAAACCA 57.972 36.000 0.00 0.00 31.46 3.67
158 238 7.466804 AGTAGGGTCATCTATTTTGAAACCAA 58.533 34.615 0.00 0.00 31.46 3.67
159 239 6.840780 AGGGTCATCTATTTTGAAACCAAG 57.159 37.500 0.00 0.00 31.46 3.61
160 240 5.716703 AGGGTCATCTATTTTGAAACCAAGG 59.283 40.000 0.00 0.00 31.46 3.61
161 241 5.105351 GGGTCATCTATTTTGAAACCAAGGG 60.105 44.000 0.00 0.00 31.46 3.95
162 242 5.714806 GGTCATCTATTTTGAAACCAAGGGA 59.285 40.000 0.00 0.00 0.00 4.20
163 243 6.127619 GGTCATCTATTTTGAAACCAAGGGAG 60.128 42.308 0.00 0.00 0.00 4.30
164 244 6.434340 GTCATCTATTTTGAAACCAAGGGAGT 59.566 38.462 0.00 0.00 0.00 3.85
165 245 7.610305 GTCATCTATTTTGAAACCAAGGGAGTA 59.390 37.037 0.00 0.00 0.00 2.59
166 246 7.610305 TCATCTATTTTGAAACCAAGGGAGTAC 59.390 37.037 0.00 0.00 0.00 2.73
167 247 7.086685 TCTATTTTGAAACCAAGGGAGTACT 57.913 36.000 0.00 0.00 0.00 2.73
168 248 7.166167 TCTATTTTGAAACCAAGGGAGTACTC 58.834 38.462 14.87 14.87 0.00 2.59
169 249 3.396260 TTGAAACCAAGGGAGTACTCG 57.604 47.619 16.56 5.07 0.00 4.18
170 250 2.322658 TGAAACCAAGGGAGTACTCGT 58.677 47.619 16.56 5.71 0.00 4.18
171 251 2.036733 TGAAACCAAGGGAGTACTCGTG 59.963 50.000 16.56 13.43 0.00 4.35
172 252 2.005370 AACCAAGGGAGTACTCGTGA 57.995 50.000 16.56 0.00 0.00 4.35
173 253 1.546961 ACCAAGGGAGTACTCGTGAG 58.453 55.000 16.56 6.88 0.00 3.51
174 254 1.075050 ACCAAGGGAGTACTCGTGAGA 59.925 52.381 16.56 0.00 39.12 3.27
175 255 1.473278 CCAAGGGAGTACTCGTGAGAC 59.527 57.143 16.56 1.56 35.39 3.36
176 256 2.438411 CAAGGGAGTACTCGTGAGACT 58.562 52.381 16.56 5.15 35.39 3.24
187 267 3.175152 CTCGTGAGACTGCTGTGATTAC 58.825 50.000 0.00 0.00 35.39 1.89
188 268 1.914051 CGTGAGACTGCTGTGATTACG 59.086 52.381 0.00 4.86 0.00 3.18
189 269 2.414161 CGTGAGACTGCTGTGATTACGA 60.414 50.000 13.75 0.00 0.00 3.43
291 371 5.763698 GTCTGACTTTTTAGCAGGTAGGTTT 59.236 40.000 0.00 0.00 0.00 3.27
292 372 6.262496 GTCTGACTTTTTAGCAGGTAGGTTTT 59.738 38.462 0.00 0.00 0.00 2.43
293 373 6.262273 TCTGACTTTTTAGCAGGTAGGTTTTG 59.738 38.462 0.00 0.00 0.00 2.44
294 374 5.196341 ACTTTTTAGCAGGTAGGTTTTGC 57.804 39.130 0.00 0.00 38.09 3.68
296 376 5.362717 ACTTTTTAGCAGGTAGGTTTTGCTT 59.637 36.000 3.36 0.00 45.28 3.91
297 377 5.862678 TTTTAGCAGGTAGGTTTTGCTTT 57.137 34.783 3.36 0.00 45.28 3.51
298 378 5.862678 TTTAGCAGGTAGGTTTTGCTTTT 57.137 34.783 3.36 0.00 45.28 2.27
299 379 5.862678 TTAGCAGGTAGGTTTTGCTTTTT 57.137 34.783 3.36 0.00 45.28 1.94
300 380 6.963083 TTAGCAGGTAGGTTTTGCTTTTTA 57.037 33.333 3.36 0.00 45.28 1.52
305 385 5.009610 CAGGTAGGTTTTGCTTTTTAGCAGA 59.990 40.000 0.00 0.00 46.21 4.26
404 487 7.308435 CGGCTGTTCTCTGAAGAAAAATAAAT 58.692 34.615 0.00 0.00 43.04 1.40
584 686 0.391228 TTGGCTTGCGTACTCAGTCA 59.609 50.000 0.00 0.00 0.00 3.41
611 713 2.182827 AGCTGGCTCTTGATGTCAGTA 58.817 47.619 0.00 0.00 0.00 2.74
613 715 3.199508 AGCTGGCTCTTGATGTCAGTAAT 59.800 43.478 0.00 0.00 0.00 1.89
615 717 4.034975 GCTGGCTCTTGATGTCAGTAATTC 59.965 45.833 0.00 0.00 0.00 2.17
624 726 8.939929 TCTTGATGTCAGTAATTCAATTCTCAC 58.060 33.333 0.00 0.00 0.00 3.51
639 741 5.741388 ATTCTCACGAAATATTCACCTGC 57.259 39.130 0.00 0.00 31.91 4.85
645 747 3.370978 ACGAAATATTCACCTGCGTTCAG 59.629 43.478 0.00 0.00 40.02 3.02
671 773 0.880278 TTCTGACTTGTGACAGCGGC 60.880 55.000 0.00 0.00 36.26 6.53
708 810 9.166173 CTGATCACTTATGTAAATCCAGTTTGA 57.834 33.333 0.00 0.00 0.00 2.69
732 834 0.739462 TTGCCTGCGTAATCTCACGG 60.739 55.000 0.00 0.00 42.18 4.94
787 891 2.811317 CGTTGACCTCGCTCCTGC 60.811 66.667 0.00 0.00 0.00 4.85
789 893 2.604686 TTGACCTCGCTCCTGCCT 60.605 61.111 0.00 0.00 35.36 4.75
790 894 1.304962 TTGACCTCGCTCCTGCCTA 60.305 57.895 0.00 0.00 35.36 3.93
791 895 1.605058 TTGACCTCGCTCCTGCCTAC 61.605 60.000 0.00 0.00 35.36 3.18
794 898 3.905678 CTCGCTCCTGCCTACCCG 61.906 72.222 0.00 0.00 35.36 5.28
896 1008 3.243501 ACCATGAAAATGACACAGCACAC 60.244 43.478 0.00 0.00 0.00 3.82
906 1018 2.878406 GACACAGCACACAACAATACCT 59.122 45.455 0.00 0.00 0.00 3.08
937 1055 0.877071 CTAAACACACTGGCTGGCTG 59.123 55.000 6.56 6.56 0.00 4.85
939 1057 4.962836 ACACACTGGCTGGCTGGC 62.963 66.667 11.09 11.09 42.18 4.85
940 1058 4.655647 CACACTGGCTGGCTGGCT 62.656 66.667 18.27 0.00 42.34 4.75
948 1066 3.720601 CTGGCTGGCTGGCTGGTA 61.721 66.667 18.27 0.00 42.34 3.25
949 1067 3.694058 CTGGCTGGCTGGCTGGTAG 62.694 68.421 18.27 4.27 42.34 3.18
951 1069 4.106925 GCTGGCTGGCTGGTAGCT 62.107 66.667 9.98 0.00 41.99 3.32
952 1070 2.124819 CTGGCTGGCTGGTAGCTG 60.125 66.667 0.00 0.00 41.99 4.24
955 1073 2.437359 GCTGGCTGGTAGCTGGTG 60.437 66.667 0.00 0.00 41.99 4.17
962 1080 4.425772 TGGCTGGTAGCTGGTGTATATAT 58.574 43.478 0.00 0.00 41.99 0.86
1043 1179 3.093057 CGAAGAAGAAGAGGAGGAGGAA 58.907 50.000 0.00 0.00 0.00 3.36
1058 1197 2.224892 GGAGGAAGAGGAAGCAAGGTTT 60.225 50.000 0.00 0.00 0.00 3.27
1114 1313 3.265221 TGATCAGCAACCTCCATTCTTCT 59.735 43.478 0.00 0.00 0.00 2.85
1156 1379 1.160329 AATGGGCGATCGTTAGCTGC 61.160 55.000 17.81 0.00 0.00 5.25
1326 1558 0.323633 TTGATGCCACTGTGGATGGG 60.324 55.000 30.23 3.70 40.96 4.00
1350 1585 1.810030 GGCCTTGTCGGACGATGAC 60.810 63.158 3.34 0.00 36.88 3.06
1722 1960 2.186125 GGTAACGGCTTCGAGGGG 59.814 66.667 0.00 0.00 37.63 4.79
1902 2140 2.281484 GACCTCTTTGCCGCCACA 60.281 61.111 0.00 0.00 0.00 4.17
2000 2238 2.192443 CCGCCTCGACCTCTCCTA 59.808 66.667 0.00 0.00 0.00 2.94
2226 2464 1.890041 CGACCTGGGCGTCAACAAA 60.890 57.895 15.33 0.00 32.74 2.83
2451 2689 0.250295 TGCTCACCAAGAACTTCCGG 60.250 55.000 0.00 0.00 0.00 5.14
3129 3367 1.214062 CTTCACCTTCTCGAGCGCT 59.786 57.895 11.27 11.27 0.00 5.92
3190 3428 2.654877 GGAAGTGCGACCGGAAGA 59.345 61.111 9.46 0.00 0.00 2.87
3191 3429 1.218316 GGAAGTGCGACCGGAAGAT 59.782 57.895 9.46 0.00 0.00 2.40
3615 3856 2.492090 CTCTCCGGCGACTTCCAG 59.508 66.667 9.30 0.00 0.00 3.86
4296 4549 2.683933 GAGGACCCCAAGGCGAGA 60.684 66.667 0.00 0.00 36.11 4.04
4414 4680 6.307031 ACTGAATCGATACTACAGTAGCAG 57.693 41.667 18.71 6.75 39.52 4.24
4415 4681 5.109662 TGAATCGATACTACAGTAGCAGC 57.890 43.478 7.57 0.00 36.78 5.25
4431 4714 1.996191 GCAGCTAGCTGTGACAGTAAC 59.004 52.381 37.91 19.22 45.24 2.50
4459 4745 6.491394 TCGTGTAAATTTTGACAAGAGTTGG 58.509 36.000 0.00 0.00 31.69 3.77
4498 4784 6.220726 TGAATGGACGATGATTAACTCAGA 57.779 37.500 0.00 0.00 37.28 3.27
4524 4810 3.525268 TGCTAAATCTCAGTCGATGCA 57.475 42.857 0.00 0.00 0.00 3.96
4530 4816 7.014115 GCTAAATCTCAGTCGATGCAATATTG 58.986 38.462 11.27 11.27 0.00 1.90
4550 4836 5.940192 TTGCTGACGTTTTACATGAAGAT 57.060 34.783 0.00 0.00 0.00 2.40
4561 4847 7.957484 CGTTTTACATGAAGATCTGTGTAAAGG 59.043 37.037 24.79 20.41 43.63 3.11
4564 4850 8.547967 TTACATGAAGATCTGTGTAAAGGTTC 57.452 34.615 18.69 2.61 34.98 3.62
4565 4851 6.773638 ACATGAAGATCTGTGTAAAGGTTCT 58.226 36.000 0.00 0.00 0.00 3.01
4566 4852 7.227156 ACATGAAGATCTGTGTAAAGGTTCTT 58.773 34.615 0.00 0.00 0.00 2.52
4568 4854 7.496529 TGAAGATCTGTGTAAAGGTTCTTTG 57.503 36.000 0.00 0.00 0.00 2.77
4569 4855 7.279615 TGAAGATCTGTGTAAAGGTTCTTTGA 58.720 34.615 0.00 0.00 0.00 2.69
4570 4856 7.939039 TGAAGATCTGTGTAAAGGTTCTTTGAT 59.061 33.333 0.00 0.00 0.00 2.57
4572 4858 8.697507 AGATCTGTGTAAAGGTTCTTTGATTT 57.302 30.769 0.00 0.00 0.00 2.17
4573 4859 9.136323 AGATCTGTGTAAAGGTTCTTTGATTTT 57.864 29.630 0.00 0.00 0.00 1.82
4574 4860 9.399403 GATCTGTGTAAAGGTTCTTTGATTTTC 57.601 33.333 3.44 0.00 0.00 2.29
4575 4861 8.519799 TCTGTGTAAAGGTTCTTTGATTTTCT 57.480 30.769 3.44 0.00 0.00 2.52
4576 4862 8.966868 TCTGTGTAAAGGTTCTTTGATTTTCTT 58.033 29.630 3.44 0.00 0.00 2.52
4577 4863 9.586435 CTGTGTAAAGGTTCTTTGATTTTCTTT 57.414 29.630 3.44 0.00 0.00 2.52
4578 4864 9.581099 TGTGTAAAGGTTCTTTGATTTTCTTTC 57.419 29.630 3.44 0.00 0.00 2.62
4579 4865 9.803315 GTGTAAAGGTTCTTTGATTTTCTTTCT 57.197 29.630 3.44 0.00 0.00 2.52
4652 4938 1.410882 GACTGAGATCTAGCCACACCC 59.589 57.143 0.00 0.00 0.00 4.61
4661 4948 4.919774 TCTAGCCACACCCTTAATTCAA 57.080 40.909 0.00 0.00 0.00 2.69
4684 4971 0.035317 TTCAACTCTGCACCGCATCT 59.965 50.000 0.00 0.00 38.13 2.90
4689 4976 1.550524 ACTCTGCACCGCATCTAAGAA 59.449 47.619 0.00 0.00 38.13 2.52
4694 4981 2.289382 TGCACCGCATCTAAGAAGTTGA 60.289 45.455 0.00 0.00 31.71 3.18
4724 5011 9.559958 AAATAAGAACAAGCAATACATTTCTCG 57.440 29.630 0.00 0.00 0.00 4.04
4752 5039 4.001618 ACAAACCAACAAGCAACACTTT 57.998 36.364 0.00 0.00 36.04 2.66
4755 5042 5.049749 ACAAACCAACAAGCAACACTTTTTC 60.050 36.000 0.00 0.00 36.04 2.29
4756 5043 3.595173 ACCAACAAGCAACACTTTTTCC 58.405 40.909 0.00 0.00 36.04 3.13
4779 5067 7.116075 TCCGCCAAAAGGCAATACATATATAT 58.884 34.615 7.34 0.00 34.62 0.86
4891 5180 1.955080 CCAGATCCGTAGACCACCTAC 59.045 57.143 0.00 0.00 43.34 3.18
4907 5196 1.404391 CCTACCGACGACTACAAGCAT 59.596 52.381 0.00 0.00 0.00 3.79
4923 5212 0.523072 GCATTGAAGCGAGCCAAAGA 59.477 50.000 0.00 0.00 0.00 2.52
5038 5329 0.678366 ACGCACCAGAACAACAACCA 60.678 50.000 0.00 0.00 0.00 3.67
5042 5333 0.034863 ACCAGAACAACAACCACCGT 60.035 50.000 0.00 0.00 0.00 4.83
5044 5335 1.374560 CAGAACAACAACCACCGTCA 58.625 50.000 0.00 0.00 0.00 4.35
5051 5342 1.604604 ACAACCACCGTCAATGAAGG 58.395 50.000 13.58 13.58 37.23 3.46
5056 5347 0.874390 CACCGTCAATGAAGGGTGTG 59.126 55.000 18.84 5.19 45.70 3.82
5085 5376 2.915604 AGGATCCAACCTGAAGACACAT 59.084 45.455 15.82 0.00 39.01 3.21
5254 5575 4.202367 CCTTTCTGAGTAGGACACAAACCT 60.202 45.833 2.65 0.00 41.05 3.50
5260 5585 5.991861 TGAGTAGGACACAAACCTTAACAA 58.008 37.500 0.00 0.00 38.76 2.83
5304 5632 2.856988 AGCCCTCCCACCGGAAAA 60.857 61.111 9.46 0.00 37.86 2.29
5439 5780 4.813526 CGTCTCGCCCGTGTCTCG 62.814 72.222 0.00 0.00 39.52 4.04
5448 5789 2.202362 CGTGTCTCGGCTGAGTCG 60.202 66.667 21.88 19.13 43.09 4.18
5449 5790 2.677979 CGTGTCTCGGCTGAGTCGA 61.678 63.158 21.88 9.45 43.09 4.20
5450 5791 1.803943 GTGTCTCGGCTGAGTCGAT 59.196 57.895 21.88 0.00 39.46 3.59
5451 5792 1.015109 GTGTCTCGGCTGAGTCGATA 58.985 55.000 21.88 0.00 39.46 2.92
5452 5793 1.604755 GTGTCTCGGCTGAGTCGATAT 59.395 52.381 21.88 0.00 39.46 1.63
5453 5794 2.806818 GTGTCTCGGCTGAGTCGATATA 59.193 50.000 21.88 0.00 39.46 0.86
5454 5795 3.437395 GTGTCTCGGCTGAGTCGATATAT 59.563 47.826 21.88 0.00 39.46 0.86
5455 5796 4.630505 GTGTCTCGGCTGAGTCGATATATA 59.369 45.833 21.88 0.00 39.46 0.86
5456 5797 4.630505 TGTCTCGGCTGAGTCGATATATAC 59.369 45.833 21.88 9.96 39.46 1.47
5457 5798 4.871557 GTCTCGGCTGAGTCGATATATACT 59.128 45.833 21.88 0.00 39.46 2.12
5458 5799 4.870991 TCTCGGCTGAGTCGATATATACTG 59.129 45.833 21.88 0.00 39.46 2.74
5459 5800 4.576879 TCGGCTGAGTCGATATATACTGT 58.423 43.478 4.48 0.00 33.73 3.55
5460 5801 5.727434 TCGGCTGAGTCGATATATACTGTA 58.273 41.667 4.48 0.00 33.73 2.74
5461 5802 6.346896 TCGGCTGAGTCGATATATACTGTAT 58.653 40.000 4.48 5.53 33.73 2.29
5462 5803 6.822170 TCGGCTGAGTCGATATATACTGTATT 59.178 38.462 4.48 0.00 33.73 1.89
5463 5804 7.336176 TCGGCTGAGTCGATATATACTGTATTT 59.664 37.037 4.48 0.79 33.73 1.40
5464 5805 8.610035 CGGCTGAGTCGATATATACTGTATTTA 58.390 37.037 0.00 3.16 29.41 1.40
5465 5806 9.938670 GGCTGAGTCGATATATACTGTATTTAG 57.061 37.037 5.52 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.236674 TGCATCAAAAATTCAGAAAACAGTG 57.763 32.000 0.00 0.00 0.00 3.66
39 40 7.914346 GCTGAATTTCCTGTGAGAATTATTGAG 59.086 37.037 0.00 0.00 0.00 3.02
43 121 6.320672 CCAGCTGAATTTCCTGTGAGAATTAT 59.679 38.462 17.39 0.00 0.00 1.28
53 131 2.205022 TGGACCAGCTGAATTTCCTG 57.795 50.000 17.39 0.00 0.00 3.86
55 133 2.353109 GCTTTGGACCAGCTGAATTTCC 60.353 50.000 17.39 15.03 34.15 3.13
56 134 2.560105 AGCTTTGGACCAGCTGAATTTC 59.440 45.455 17.39 5.68 46.25 2.17
66 146 1.004745 GGGAGAATGAGCTTTGGACCA 59.995 52.381 0.00 0.00 0.00 4.02
70 150 1.745141 CGGAGGGAGAATGAGCTTTGG 60.745 57.143 0.00 0.00 0.00 3.28
84 164 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
85 165 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
86 166 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
88 168 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
89 169 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
90 170 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
91 171 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
92 172 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
94 174 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
95 175 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
96 176 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
97 177 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
98 178 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
99 179 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
100 180 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
101 181 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
102 182 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
103 183 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
116 196 9.586732 TGACCCTACTTTGTACTAAAGTTAGTA 57.413 33.333 20.78 6.81 43.36 1.82
117 197 8.482852 TGACCCTACTTTGTACTAAAGTTAGT 57.517 34.615 20.78 16.72 45.39 2.24
118 198 9.583765 GATGACCCTACTTTGTACTAAAGTTAG 57.416 37.037 20.78 16.36 40.58 2.34
119 199 9.317827 AGATGACCCTACTTTGTACTAAAGTTA 57.682 33.333 20.78 11.09 40.58 2.24
120 200 8.203681 AGATGACCCTACTTTGTACTAAAGTT 57.796 34.615 20.78 9.27 40.58 2.66
121 201 7.793948 AGATGACCCTACTTTGTACTAAAGT 57.206 36.000 19.97 19.97 42.53 2.66
126 206 8.822805 TCAAAATAGATGACCCTACTTTGTACT 58.177 33.333 0.00 0.00 37.23 2.73
127 207 9.444600 TTCAAAATAGATGACCCTACTTTGTAC 57.555 33.333 0.00 0.00 37.23 2.90
129 209 8.793592 GTTTCAAAATAGATGACCCTACTTTGT 58.206 33.333 0.00 0.00 37.23 2.83
130 210 8.244113 GGTTTCAAAATAGATGACCCTACTTTG 58.756 37.037 0.00 0.00 37.26 2.77
131 211 7.947890 TGGTTTCAAAATAGATGACCCTACTTT 59.052 33.333 0.00 0.00 0.00 2.66
132 212 7.466804 TGGTTTCAAAATAGATGACCCTACTT 58.533 34.615 0.00 0.00 0.00 2.24
133 213 7.027874 TGGTTTCAAAATAGATGACCCTACT 57.972 36.000 0.00 0.00 0.00 2.57
134 214 7.148069 CCTTGGTTTCAAAATAGATGACCCTAC 60.148 40.741 0.00 0.00 31.77 3.18
135 215 6.889722 CCTTGGTTTCAAAATAGATGACCCTA 59.110 38.462 0.00 0.00 31.77 3.53
136 216 5.716703 CCTTGGTTTCAAAATAGATGACCCT 59.283 40.000 0.00 0.00 31.77 4.34
137 217 5.105351 CCCTTGGTTTCAAAATAGATGACCC 60.105 44.000 0.00 0.00 31.77 4.46
138 218 5.714806 TCCCTTGGTTTCAAAATAGATGACC 59.285 40.000 0.00 0.00 31.77 4.02
139 219 6.434340 ACTCCCTTGGTTTCAAAATAGATGAC 59.566 38.462 0.00 0.00 31.77 3.06
140 220 6.552008 ACTCCCTTGGTTTCAAAATAGATGA 58.448 36.000 0.00 0.00 31.77 2.92
141 221 6.840780 ACTCCCTTGGTTTCAAAATAGATG 57.159 37.500 0.00 0.00 31.77 2.90
142 222 7.699878 AGTACTCCCTTGGTTTCAAAATAGAT 58.300 34.615 0.00 0.00 31.77 1.98
143 223 7.086685 AGTACTCCCTTGGTTTCAAAATAGA 57.913 36.000 0.00 0.00 31.77 1.98
144 224 6.092259 CGAGTACTCCCTTGGTTTCAAAATAG 59.908 42.308 17.23 0.00 31.77 1.73
145 225 5.935789 CGAGTACTCCCTTGGTTTCAAAATA 59.064 40.000 17.23 0.00 31.77 1.40
146 226 4.760204 CGAGTACTCCCTTGGTTTCAAAAT 59.240 41.667 17.23 0.00 31.77 1.82
147 227 4.131596 CGAGTACTCCCTTGGTTTCAAAA 58.868 43.478 17.23 0.00 31.77 2.44
148 228 3.135167 ACGAGTACTCCCTTGGTTTCAAA 59.865 43.478 17.23 0.00 31.77 2.69
149 229 2.701951 ACGAGTACTCCCTTGGTTTCAA 59.298 45.455 17.23 0.00 0.00 2.69
150 230 2.036733 CACGAGTACTCCCTTGGTTTCA 59.963 50.000 17.23 0.00 0.00 2.69
151 231 2.298163 TCACGAGTACTCCCTTGGTTTC 59.702 50.000 17.23 0.00 0.00 2.78
152 232 2.299297 CTCACGAGTACTCCCTTGGTTT 59.701 50.000 17.23 0.00 0.00 3.27
153 233 1.893801 CTCACGAGTACTCCCTTGGTT 59.106 52.381 17.23 0.00 0.00 3.67
154 234 1.075050 TCTCACGAGTACTCCCTTGGT 59.925 52.381 17.23 5.95 0.00 3.67
155 235 1.473278 GTCTCACGAGTACTCCCTTGG 59.527 57.143 17.23 5.29 0.00 3.61
156 236 2.162608 CAGTCTCACGAGTACTCCCTTG 59.837 54.545 17.23 11.59 0.00 3.61
157 237 2.438411 CAGTCTCACGAGTACTCCCTT 58.562 52.381 17.23 0.00 0.00 3.95
158 238 1.951424 GCAGTCTCACGAGTACTCCCT 60.951 57.143 17.23 0.00 0.00 4.20
159 239 0.452585 GCAGTCTCACGAGTACTCCC 59.547 60.000 17.23 0.00 0.00 4.30
160 240 1.131504 CAGCAGTCTCACGAGTACTCC 59.868 57.143 17.23 1.96 0.00 3.85
161 241 1.807742 ACAGCAGTCTCACGAGTACTC 59.192 52.381 13.18 13.18 0.00 2.59
162 242 1.537638 CACAGCAGTCTCACGAGTACT 59.462 52.381 0.00 0.00 0.00 2.73
163 243 1.535896 TCACAGCAGTCTCACGAGTAC 59.464 52.381 0.00 0.00 0.00 2.73
164 244 1.892209 TCACAGCAGTCTCACGAGTA 58.108 50.000 0.00 0.00 0.00 2.59
165 245 1.252175 ATCACAGCAGTCTCACGAGT 58.748 50.000 0.00 0.00 0.00 4.18
166 246 2.360553 AATCACAGCAGTCTCACGAG 57.639 50.000 0.00 0.00 0.00 4.18
167 247 2.414161 CGTAATCACAGCAGTCTCACGA 60.414 50.000 0.00 0.00 0.00 4.35
168 248 1.914051 CGTAATCACAGCAGTCTCACG 59.086 52.381 0.00 0.00 0.00 4.35
169 249 2.917971 GTCGTAATCACAGCAGTCTCAC 59.082 50.000 0.00 0.00 0.00 3.51
170 250 2.820197 AGTCGTAATCACAGCAGTCTCA 59.180 45.455 0.00 0.00 0.00 3.27
171 251 3.119814 TCAGTCGTAATCACAGCAGTCTC 60.120 47.826 0.00 0.00 0.00 3.36
172 252 2.820197 TCAGTCGTAATCACAGCAGTCT 59.180 45.455 0.00 0.00 0.00 3.24
173 253 3.217599 TCAGTCGTAATCACAGCAGTC 57.782 47.619 0.00 0.00 0.00 3.51
174 254 3.193479 TGATCAGTCGTAATCACAGCAGT 59.807 43.478 0.00 0.00 0.00 4.40
175 255 3.774066 TGATCAGTCGTAATCACAGCAG 58.226 45.455 0.00 0.00 0.00 4.24
176 256 3.866883 TGATCAGTCGTAATCACAGCA 57.133 42.857 0.00 0.00 0.00 4.41
187 267 2.867287 ATCTGCTGAGTGATCAGTCG 57.133 50.000 22.50 18.01 39.76 4.18
188 268 5.261209 ACTAATCTGCTGAGTGATCAGTC 57.739 43.478 21.57 21.57 39.76 3.51
189 269 5.654209 TGTACTAATCTGCTGAGTGATCAGT 59.346 40.000 1.67 1.67 39.76 3.41
200 280 3.865745 GCGTGTGATTGTACTAATCTGCT 59.134 43.478 14.81 0.00 0.00 4.24
201 281 3.865745 AGCGTGTGATTGTACTAATCTGC 59.134 43.478 14.81 13.15 0.00 4.26
206 286 4.242475 CTCCAAGCGTGTGATTGTACTAA 58.758 43.478 0.00 0.00 39.84 2.24
291 371 4.078537 TGCACCTATCTGCTAAAAAGCAA 58.921 39.130 1.28 0.00 44.88 3.91
292 372 3.684908 TGCACCTATCTGCTAAAAAGCA 58.315 40.909 0.00 0.00 43.22 3.91
293 373 4.604976 CATGCACCTATCTGCTAAAAAGC 58.395 43.478 0.00 0.00 38.07 3.51
294 374 4.096833 TGCATGCACCTATCTGCTAAAAAG 59.903 41.667 18.46 0.00 38.07 2.27
295 375 4.015764 TGCATGCACCTATCTGCTAAAAA 58.984 39.130 18.46 0.00 38.07 1.94
296 376 3.378112 GTGCATGCACCTATCTGCTAAAA 59.622 43.478 35.69 0.00 40.79 1.52
297 377 2.945008 GTGCATGCACCTATCTGCTAAA 59.055 45.455 35.69 0.00 40.79 1.85
298 378 2.093021 TGTGCATGCACCTATCTGCTAA 60.093 45.455 40.01 20.03 45.63 3.09
299 379 1.485895 TGTGCATGCACCTATCTGCTA 59.514 47.619 40.01 20.72 45.63 3.49
300 380 0.253894 TGTGCATGCACCTATCTGCT 59.746 50.000 40.01 0.00 45.63 4.24
305 385 1.561076 TCTTCCTGTGCATGCACCTAT 59.439 47.619 40.01 0.00 45.63 2.57
321 401 0.107945 ACATCGGCAGCTTCCTCTTC 60.108 55.000 0.00 0.00 0.00 2.87
404 487 9.146984 GAGCAAGTGTGTACAGTACATTTTATA 57.853 33.333 16.57 0.00 41.34 0.98
412 495 3.005472 TCCTGAGCAAGTGTGTACAGTAC 59.995 47.826 3.49 3.49 32.29 2.73
413 496 3.227614 TCCTGAGCAAGTGTGTACAGTA 58.772 45.455 0.00 0.00 32.29 2.74
414 497 2.039418 TCCTGAGCAAGTGTGTACAGT 58.961 47.619 0.00 0.00 32.29 3.55
415 498 2.820059 TCCTGAGCAAGTGTGTACAG 57.180 50.000 0.00 0.00 33.23 2.74
416 499 3.111853 CTTCCTGAGCAAGTGTGTACA 57.888 47.619 0.00 0.00 0.00 2.90
536 634 8.279800 CGCAGGTCTATCTATTTATCTATCGAG 58.720 40.741 0.00 0.00 0.00 4.04
538 636 8.065407 GTCGCAGGTCTATCTATTTATCTATCG 58.935 40.741 0.00 0.00 0.00 2.92
584 686 3.280295 CATCAAGAGCCAGCTTCAGAAT 58.720 45.455 0.00 0.00 0.00 2.40
624 726 3.616821 TCTGAACGCAGGTGAATATTTCG 59.383 43.478 0.00 0.00 42.53 3.46
693 795 6.719370 AGGCAAGTAATCAAACTGGATTTACA 59.281 34.615 0.00 0.00 38.41 2.41
702 804 2.504367 ACGCAGGCAAGTAATCAAACT 58.496 42.857 0.00 0.00 0.00 2.66
703 805 2.989422 ACGCAGGCAAGTAATCAAAC 57.011 45.000 0.00 0.00 0.00 2.93
708 810 3.871594 GTGAGATTACGCAGGCAAGTAAT 59.128 43.478 10.53 10.53 43.70 1.89
712 814 0.647410 CGTGAGATTACGCAGGCAAG 59.353 55.000 0.00 0.00 37.24 4.01
787 891 3.159347 GGTAGGGTGCCGGGTAGG 61.159 72.222 2.18 0.00 44.97 3.18
789 893 2.364579 CAGGTAGGGTGCCGGGTA 60.365 66.667 2.18 0.00 0.00 3.69
790 894 4.326227 TCAGGTAGGGTGCCGGGT 62.326 66.667 2.18 0.00 0.00 5.28
791 895 3.782443 GTCAGGTAGGGTGCCGGG 61.782 72.222 2.18 0.00 0.00 5.73
794 898 1.612442 TCAGGTCAGGTAGGGTGCC 60.612 63.158 0.00 0.00 0.00 5.01
797 901 0.252284 CAGGTCAGGTCAGGTAGGGT 60.252 60.000 0.00 0.00 0.00 4.34
896 1008 4.585162 AGACTAGATCGGGAGGTATTGTTG 59.415 45.833 0.00 0.00 0.00 3.33
906 1018 4.398358 CAGTGTGTTTAGACTAGATCGGGA 59.602 45.833 0.00 0.00 0.00 5.14
937 1055 3.721706 ACCAGCTACCAGCCAGCC 61.722 66.667 0.00 0.00 43.77 4.85
939 1057 0.833287 ATACACCAGCTACCAGCCAG 59.167 55.000 0.00 0.00 43.77 4.85
940 1058 2.168458 TATACACCAGCTACCAGCCA 57.832 50.000 0.00 0.00 43.77 4.75
942 1060 6.525578 TGTATATATACACCAGCTACCAGC 57.474 41.667 19.51 0.00 38.74 4.85
1043 1179 3.149981 GCTAACAAACCTTGCTTCCTCT 58.850 45.455 0.00 0.00 0.00 3.69
1058 1197 2.173782 TGGGTTTGACTCTTGGCTAACA 59.826 45.455 0.00 0.00 0.00 2.41
1141 1364 0.657840 ATTTGCAGCTAACGATCGCC 59.342 50.000 16.60 1.05 0.00 5.54
1156 1379 3.690685 TACCTCGCCCCGCCATTTG 62.691 63.158 0.00 0.00 0.00 2.32
1208 1440 3.906649 GCGACAGCAGCACGATCG 61.907 66.667 14.88 14.88 44.35 3.69
1339 1571 4.170062 GCCGTCGTCATCGTCCGA 62.170 66.667 0.00 0.00 38.33 4.55
1341 1573 2.579787 CAGCCGTCGTCATCGTCC 60.580 66.667 0.00 0.00 38.33 4.79
1707 1945 3.777910 GGCCCCTCGAAGCCGTTA 61.778 66.667 5.15 0.00 39.87 3.18
1791 2029 3.839432 GGGAAGTCGCCGGAGAGG 61.839 72.222 8.65 0.00 44.97 3.69
1881 2119 3.479269 GCGGCAAAGAGGTCGTCG 61.479 66.667 0.00 0.00 38.35 5.12
1884 2122 3.423154 GTGGCGGCAAAGAGGTCG 61.423 66.667 15.50 0.00 39.28 4.79
1902 2140 2.491022 GGAGAGGTACCGCAGCGAT 61.491 63.158 18.75 0.00 0.00 4.58
2187 2425 2.950309 GAGGTAGACGAGGCTATTGACA 59.050 50.000 0.00 0.00 0.00 3.58
2226 2464 2.919043 GGGATGAGGCCCGTGAAT 59.081 61.111 0.00 0.00 38.58 2.57
2563 2801 1.188219 TCGAGCACCTTGAGCTTCCT 61.188 55.000 0.00 0.00 43.58 3.36
2751 2989 0.687354 GGAAGTCCTGCACCTTCTGA 59.313 55.000 13.02 0.00 37.73 3.27
2752 2990 0.322008 GGGAAGTCCTGCACCTTCTG 60.322 60.000 13.02 0.00 37.73 3.02
3129 3367 4.011517 GGGTTCCCGGCGAAGTCA 62.012 66.667 9.30 0.00 0.00 3.41
3190 3428 1.620819 GTCCGTGGCCTGATCATCTAT 59.379 52.381 3.32 0.00 0.00 1.98
3191 3429 1.040646 GTCCGTGGCCTGATCATCTA 58.959 55.000 3.32 0.00 0.00 1.98
3228 3466 1.745489 GCTCCTTCGGCCGTCATTT 60.745 57.895 27.15 0.00 0.00 2.32
3346 3584 2.032681 GCAGGCGTTGTCCTCCTT 59.967 61.111 0.00 0.00 33.25 3.36
3378 3616 1.006571 GGTGCTTTCCTCGTCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
3450 3688 1.707239 CCGTCGTCTCCTCCTCTTCG 61.707 65.000 0.00 0.00 0.00 3.79
3492 3733 2.284112 AAGTCCCCCGTCGCCTTA 60.284 61.111 0.00 0.00 0.00 2.69
3615 3856 2.510238 AACTCGCGCTCCATCTGC 60.510 61.111 5.56 0.00 0.00 4.26
4378 4640 2.719556 CGATTCAGTTATCTACCGTGCG 59.280 50.000 0.00 0.00 0.00 5.34
4380 4642 6.900189 AGTATCGATTCAGTTATCTACCGTG 58.100 40.000 1.71 0.00 0.00 4.94
4382 4644 8.026341 TGTAGTATCGATTCAGTTATCTACCG 57.974 38.462 1.71 0.00 0.00 4.02
4383 4645 9.001542 ACTGTAGTATCGATTCAGTTATCTACC 57.998 37.037 1.71 0.00 36.17 3.18
4414 4680 4.109050 GAGATGTTACTGTCACAGCTAGC 58.891 47.826 12.33 6.62 40.95 3.42
4415 4681 4.142578 ACGAGATGTTACTGTCACAGCTAG 60.143 45.833 12.33 14.15 40.95 3.42
4431 4714 7.576236 ACTCTTGTCAAAATTTACACGAGATG 58.424 34.615 23.82 16.58 41.85 2.90
4459 4745 7.009815 TCGTCCATTCAATCTTTATACACGAAC 59.990 37.037 0.00 0.00 0.00 3.95
4498 4784 3.706594 TCGACTGAGATTTAGCAATCCCT 59.293 43.478 0.00 0.00 39.95 4.20
4524 4810 8.039603 TCTTCATGTAAAACGTCAGCAATATT 57.960 30.769 0.00 0.00 0.00 1.28
4530 4816 5.120830 ACAGATCTTCATGTAAAACGTCAGC 59.879 40.000 0.00 0.00 0.00 4.26
4533 4819 6.467723 ACACAGATCTTCATGTAAAACGTC 57.532 37.500 0.00 0.00 0.00 4.34
4536 4822 8.784043 ACCTTTACACAGATCTTCATGTAAAAC 58.216 33.333 23.82 0.00 43.35 2.43
4550 4836 8.519799 AGAAAATCAAAGAACCTTTACACAGA 57.480 30.769 0.00 0.00 0.00 3.41
4625 4911 2.415168 GGCTAGATCTCAGTCGATCGAG 59.585 54.545 20.09 8.15 43.52 4.04
4632 4918 1.410882 GGGTGTGGCTAGATCTCAGTC 59.589 57.143 0.00 0.00 0.00 3.51
4634 4920 1.786937 AGGGTGTGGCTAGATCTCAG 58.213 55.000 0.00 0.00 0.00 3.35
4636 4922 4.965200 ATTAAGGGTGTGGCTAGATCTC 57.035 45.455 0.00 0.00 0.00 2.75
4652 4938 8.490355 GGTGCAGAGTTGAAATTTTGAATTAAG 58.510 33.333 0.00 0.00 0.00 1.85
4661 4948 1.680735 TGCGGTGCAGAGTTGAAATTT 59.319 42.857 0.00 0.00 33.32 1.82
4704 4991 4.722194 TGCGAGAAATGTATTGCTTGTTC 58.278 39.130 2.53 0.00 30.62 3.18
4891 5180 1.990799 TCAATGCTTGTAGTCGTCGG 58.009 50.000 0.00 0.00 0.00 4.79
4907 5196 1.841663 GCGTCTTTGGCTCGCTTCAA 61.842 55.000 0.00 0.00 45.29 2.69
5038 5329 0.250727 CCACACCCTTCATTGACGGT 60.251 55.000 8.26 3.94 0.00 4.83
5042 5333 5.500234 CTTCTTATCCACACCCTTCATTGA 58.500 41.667 0.00 0.00 0.00 2.57
5044 5335 4.540099 TCCTTCTTATCCACACCCTTCATT 59.460 41.667 0.00 0.00 0.00 2.57
5056 5347 5.131142 TCTTCAGGTTGGATCCTTCTTATCC 59.869 44.000 14.23 0.60 42.84 2.59
5085 5376 2.191815 TCGTCGTTCGTCTTTGTTCA 57.808 45.000 0.00 0.00 40.80 3.18
5187 5508 6.209774 TGAAGATAGAATAAAGGTCTCCCCA 58.790 40.000 0.00 0.00 34.66 4.96
5301 5629 1.208165 AGAGTGGATCCCGGCCTTTT 61.208 55.000 9.90 0.00 0.00 2.27
5304 5632 2.765807 CAGAGTGGATCCCGGCCT 60.766 66.667 9.90 0.00 0.00 5.19
5431 5772 1.983196 ATCGACTCAGCCGAGACACG 61.983 60.000 3.36 6.76 42.34 4.49
5432 5773 1.015109 TATCGACTCAGCCGAGACAC 58.985 55.000 3.36 0.00 42.34 3.67
5433 5774 1.968704 ATATCGACTCAGCCGAGACA 58.031 50.000 3.36 0.00 42.34 3.41
5434 5775 4.871557 AGTATATATCGACTCAGCCGAGAC 59.128 45.833 3.36 0.00 42.34 3.36
5435 5776 4.870991 CAGTATATATCGACTCAGCCGAGA 59.129 45.833 3.36 0.00 42.34 4.04
5436 5777 4.632251 ACAGTATATATCGACTCAGCCGAG 59.368 45.833 0.00 0.00 45.49 4.63
5437 5778 4.576879 ACAGTATATATCGACTCAGCCGA 58.423 43.478 0.00 0.00 40.53 5.54
5438 5779 4.948608 ACAGTATATATCGACTCAGCCG 57.051 45.455 0.00 0.00 0.00 5.52
5439 5780 9.938670 CTAAATACAGTATATATCGACTCAGCC 57.061 37.037 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.