Multiple sequence alignment - TraesCS1D01G244300

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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 TraesCS1D01G244300 chr1D 100.000 5431 0 0 1 5431 335078413 335072983 0.000000e+00 10030
1 TraesCS1D01G244300 chr1D 89.875 800 66 7 2544 3336 465414487 465413696 0.000000e+00 1014
2 TraesCS1D01G244300 chr1D 83.944 355 34 14 2984 3336 468786824 468787157 8.780000e-83 318
3 TraesCS1D01G244300 chr1D 84.242 330 32 11 3008 3336 468789214 468789524 2.460000e-78 303
4 TraesCS1D01G244300 chr1D 83.939 330 31 12 3008 3336 468788426 468788734 4.110000e-76 296
5 TraesCS1D01G244300 chr1D 86.792 159 20 1 3688 3845 28014149 28014307 5.590000e-40 176
6 TraesCS1D01G244300 chr1B 96.284 2395 65 6 957 3336 450612735 450610350 0.000000e+00 3908
7 TraesCS1D01G244300 chr1B 95.650 1816 58 9 3577 5387 450610350 450608551 0.000000e+00 2896
8 TraesCS1D01G244300 chr1B 85.691 615 38 20 337 902 450613518 450612905 2.160000e-168 603
9 TraesCS1D01G244300 chr1A 96.228 2333 39 9 1025 3336 432637942 432635638 0.000000e+00 3775
10 TraesCS1D01G244300 chr1A 94.013 1737 72 14 3577 5302 432635638 432633923 0.000000e+00 2603
11 TraesCS1D01G244300 chr1A 92.128 343 17 6 2 339 46271072 46271409 4.920000e-130 475
12 TraesCS1D01G244300 chr1A 84.419 430 31 15 348 763 432638764 432638357 1.830000e-104 390
13 TraesCS1D01G244300 chr1A 88.387 155 8 2 5287 5431 432633773 432633619 1.550000e-40 178
14 TraesCS1D01G244300 chr7A 88.958 806 73 8 2544 3336 686308848 686309650 0.000000e+00 981
15 TraesCS1D01G244300 chr7A 92.353 340 21 5 1 336 202749509 202749847 3.810000e-131 479
16 TraesCS1D01G244300 chr7A 94.186 258 12 3 3335 3589 728413136 728412879 1.830000e-104 390
17 TraesCS1D01G244300 chr7A 91.822 269 15 7 3310 3577 217081518 217081780 8.590000e-98 368
18 TraesCS1D01G244300 chr5D 93.314 344 13 5 1 339 242952230 242952568 2.920000e-137 499
19 TraesCS1D01G244300 chr5A 93.043 345 18 3 1 339 279743055 279742711 2.920000e-137 499
20 TraesCS1D01G244300 chr2D 92.647 340 16 4 1 336 589321470 589321804 1.060000e-131 481
21 TraesCS1D01G244300 chr2D 95.918 245 9 1 3343 3587 106814881 106814638 3.940000e-106 396
22 TraesCS1D01G244300 chr2D 95.918 245 9 1 3343 3587 106818002 106817759 3.940000e-106 396
23 TraesCS1D01G244300 chr2D 94.466 253 12 2 3330 3582 114848070 114847820 6.600000e-104 388
24 TraesCS1D01G244300 chr2A 91.404 349 19 8 1 340 155748606 155748952 8.240000e-128 468
25 TraesCS1D01G244300 chr2A 90.831 349 20 5 1 339 83211875 83211529 1.780000e-124 457
26 TraesCS1D01G244300 chr2A 97.107 242 7 0 3340 3581 13032184 13031943 5.060000e-110 409
27 TraesCS1D01G244300 chr2A 92.126 254 19 1 2544 2796 762849452 762849705 1.860000e-94 357
28 TraesCS1D01G244300 chr3A 90.882 340 21 5 1 336 667309444 667309777 1.070000e-121 448
29 TraesCS1D01G244300 chr7D 90.230 348 24 7 1 339 487869359 487869013 3.860000e-121 446
30 TraesCS1D01G244300 chr7D 90.980 255 21 2 2544 2796 618433623 618433369 5.210000e-90 342
31 TraesCS1D01G244300 chr7D 83.853 353 35 12 2984 3335 618432873 618432542 3.160000e-82 316
32 TraesCS1D01G244300 chr6D 94.841 252 13 0 3336 3587 186329971 186330222 1.420000e-105 394
33 TraesCS1D01G244300 chr6D 94.821 251 12 1 3328 3578 220042514 220042763 1.830000e-104 390
34 TraesCS1D01G244300 chr6B 93.822 259 15 1 3332 3589 374208263 374208005 6.600000e-104 388
35 TraesCS1D01G244300 chr6A 84.463 354 35 9 2984 3336 536230677 536231011 1.130000e-86 331
36 TraesCS1D01G244300 chr6A 91.266 229 19 1 2557 2784 536229929 536230157 1.470000e-80 311
37 TraesCS1D01G244300 chr5B 94.891 137 7 0 2544 2680 509690176 509690312 1.180000e-51 215
38 TraesCS1D01G244300 chr5B 93.478 138 8 1 2544 2680 509824052 509823915 2.560000e-48 204


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 TraesCS1D01G244300 chr1D 335072983 335078413 5430 True 10030.000000 10030 100.000000 1 5431 1 chr1D.!!$R1 5430
1 TraesCS1D01G244300 chr1D 465413696 465414487 791 True 1014.000000 1014 89.875000 2544 3336 1 chr1D.!!$R2 792
2 TraesCS1D01G244300 chr1D 468786824 468789524 2700 False 305.666667 318 84.041667 2984 3336 3 chr1D.!!$F2 352
3 TraesCS1D01G244300 chr1B 450608551 450613518 4967 True 2469.000000 3908 92.541667 337 5387 3 chr1B.!!$R1 5050
4 TraesCS1D01G244300 chr1A 432633619 432638764 5145 True 1736.500000 3775 90.761750 348 5431 4 chr1A.!!$R1 5083
5 TraesCS1D01G244300 chr7A 686308848 686309650 802 False 981.000000 981 88.958000 2544 3336 1 chr7A.!!$F3 792
6 TraesCS1D01G244300 chr2D 106814638 106818002 3364 True 396.000000 396 95.918000 3343 3587 2 chr2D.!!$R2 244
7 TraesCS1D01G244300 chr7D 618432542 618433623 1081 True 329.000000 342 87.416500 2544 3335 2 chr7D.!!$R2 791
8 TraesCS1D01G244300 chr6A 536229929 536231011 1082 False 321.000000 331 87.864500 2557 3336 2 chr6A.!!$F1 779

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
455 472 0.033090 CGAGGCATGCAGCTCTATCA 59.967 55.000 21.36 0.00 44.79 2.15 F
939 1000 0.242555 CAAATCCCCAACCGAAACCG 59.757 55.000 0.00 0.00 0.00 4.44 F
1176 1390 1.453379 CCTCCTCCTCTTCGCCGTA 60.453 63.158 0.00 0.00 0.00 4.02 F
1764 1987 2.514803 GTGAACCCCTATGTGCACTTT 58.485 47.619 19.41 8.24 40.94 2.66 F
3471 9645 0.346932 ATACCCACACCCCTCTCCAT 59.653 55.000 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1870 0.855349 CGAAATGCTTCCCGAGATCG 59.145 55.000 0.00 0.00 39.44 3.69 R
2493 2716 0.894141 TGCCAATTTCATCAACCCCG 59.106 50.000 0.00 0.00 0.00 5.73 R
2894 3132 5.163499 ACACTGTAATCTAGTTAGGAGCTGC 60.163 44.000 0.00 0.00 0.00 5.25 R
3551 9725 0.169672 AAGATGCTCATGCGTTGCAC 59.830 50.000 5.61 1.79 43.04 4.57 R
4866 11043 1.204467 CTCTGTCTCAGTCCAGAAGGC 59.796 57.143 0.00 0.00 37.27 4.35 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
31 32 4.143333 GCCGCAGTAGCCCGAAGA 62.143 66.667 0.00 0.00 37.52 2.87
32 33 2.577059 CCGCAGTAGCCCGAAGAA 59.423 61.111 0.00 0.00 37.52 2.52
33 34 1.810030 CCGCAGTAGCCCGAAGAAC 60.810 63.158 0.00 0.00 37.52 3.01
34 35 1.810030 CGCAGTAGCCCGAAGAACC 60.810 63.158 0.00 0.00 37.52 3.62
35 36 1.449778 GCAGTAGCCCGAAGAACCC 60.450 63.158 0.00 0.00 33.58 4.11
36 37 1.221021 CAGTAGCCCGAAGAACCCC 59.779 63.158 0.00 0.00 0.00 4.95
37 38 2.186125 GTAGCCCGAAGAACCCCG 59.814 66.667 0.00 0.00 0.00 5.73
38 39 3.078836 TAGCCCGAAGAACCCCGG 61.079 66.667 0.00 0.00 44.94 5.73
66 67 4.481112 GCATGGTGGCGCGGAAAG 62.481 66.667 8.83 0.00 0.00 2.62
67 68 3.055719 CATGGTGGCGCGGAAAGT 61.056 61.111 8.83 0.00 0.00 2.66
68 69 3.055719 ATGGTGGCGCGGAAAGTG 61.056 61.111 8.83 0.00 0.00 3.16
110 111 4.821589 GCGAGGTTGCGAGGGGAG 62.822 72.222 0.00 0.00 0.00 4.30
111 112 4.148825 CGAGGTTGCGAGGGGAGG 62.149 72.222 0.00 0.00 0.00 4.30
112 113 3.787001 GAGGTTGCGAGGGGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
129 130 4.374702 GCGCGTGGCTGTGTTCTG 62.375 66.667 8.43 0.00 39.11 3.02
130 131 2.967076 CGCGTGGCTGTGTTCTGT 60.967 61.111 0.00 0.00 0.00 3.41
131 132 2.633657 GCGTGGCTGTGTTCTGTG 59.366 61.111 0.00 0.00 0.00 3.66
132 133 2.633657 CGTGGCTGTGTTCTGTGC 59.366 61.111 0.00 0.00 0.00 4.57
133 134 2.633657 GTGGCTGTGTTCTGTGCG 59.366 61.111 0.00 0.00 0.00 5.34
134 135 3.279116 TGGCTGTGTTCTGTGCGC 61.279 61.111 0.00 0.00 0.00 6.09
135 136 4.374702 GGCTGTGTTCTGTGCGCG 62.375 66.667 0.00 0.00 0.00 6.86
136 137 3.640000 GCTGTGTTCTGTGCGCGT 61.640 61.111 8.43 0.00 0.00 6.01
137 138 2.246397 CTGTGTTCTGTGCGCGTG 59.754 61.111 8.43 0.00 0.00 5.34
138 139 3.227372 CTGTGTTCTGTGCGCGTGG 62.227 63.158 8.43 0.00 0.00 4.94
139 140 4.666532 GTGTTCTGTGCGCGTGGC 62.667 66.667 8.43 0.00 43.96 5.01
154 155 2.893404 GGCGAGCGCGGGATTTTA 60.893 61.111 12.86 0.00 43.06 1.52
155 156 2.251642 GGCGAGCGCGGGATTTTAT 61.252 57.895 12.86 0.00 43.06 1.40
156 157 0.947180 GGCGAGCGCGGGATTTTATA 60.947 55.000 12.86 0.00 43.06 0.98
157 158 0.438830 GCGAGCGCGGGATTTTATAG 59.561 55.000 12.86 0.00 38.16 1.31
158 159 1.068474 CGAGCGCGGGATTTTATAGG 58.932 55.000 8.83 0.00 0.00 2.57
159 160 0.796927 GAGCGCGGGATTTTATAGGC 59.203 55.000 8.83 0.00 0.00 3.93
160 161 0.949105 AGCGCGGGATTTTATAGGCG 60.949 55.000 8.83 0.00 45.72 5.52
161 162 1.495951 CGCGGGATTTTATAGGCGC 59.504 57.895 0.00 0.00 37.08 6.53
162 163 1.495951 GCGGGATTTTATAGGCGCG 59.504 57.895 0.00 0.00 39.30 6.86
163 164 1.495951 CGGGATTTTATAGGCGCGC 59.504 57.895 25.94 25.94 0.00 6.86
164 165 1.495951 GGGATTTTATAGGCGCGCG 59.504 57.895 28.44 28.44 0.00 6.86
165 166 1.154469 GGATTTTATAGGCGCGCGC 60.154 57.895 44.40 44.40 41.06 6.86
166 167 1.507096 GATTTTATAGGCGCGCGCG 60.507 57.895 45.73 45.73 43.06 6.86
182 183 3.782042 CGAAGCCGCCAAGTCTAC 58.218 61.111 0.00 0.00 0.00 2.59
183 184 1.810030 CGAAGCCGCCAAGTCTACC 60.810 63.158 0.00 0.00 0.00 3.18
184 185 1.810030 GAAGCCGCCAAGTCTACCG 60.810 63.158 0.00 0.00 0.00 4.02
185 186 3.952628 AAGCCGCCAAGTCTACCGC 62.953 63.158 0.00 0.00 0.00 5.68
207 208 4.445545 CGTGCCGCTTTCTTCCGC 62.446 66.667 0.00 0.00 0.00 5.54
243 244 3.484547 CGCGCACGGTAAGTTCCC 61.485 66.667 8.75 0.00 34.97 3.97
249 250 2.435410 CGGTAAGTTCCCGCCACC 60.435 66.667 0.00 0.00 38.85 4.61
250 251 2.435410 GGTAAGTTCCCGCCACCG 60.435 66.667 0.00 0.00 0.00 4.94
251 252 3.122971 GTAAGTTCCCGCCACCGC 61.123 66.667 0.00 0.00 0.00 5.68
252 253 3.315949 TAAGTTCCCGCCACCGCT 61.316 61.111 0.00 0.00 0.00 5.52
253 254 3.599285 TAAGTTCCCGCCACCGCTG 62.599 63.158 0.00 0.00 0.00 5.18
290 291 2.427740 GCGCGCGCTAAAACCAAA 60.428 55.556 44.38 0.00 38.26 3.28
291 292 2.703230 GCGCGCGCTAAAACCAAAC 61.703 57.895 44.38 13.88 38.26 2.93
292 293 1.082366 CGCGCGCTAAAACCAAACT 60.082 52.632 30.48 0.00 0.00 2.66
293 294 0.659123 CGCGCGCTAAAACCAAACTT 60.659 50.000 30.48 0.00 0.00 2.66
294 295 1.483316 GCGCGCTAAAACCAAACTTT 58.517 45.000 26.67 0.00 0.00 2.66
295 296 2.652795 GCGCGCTAAAACCAAACTTTA 58.347 42.857 26.67 0.00 0.00 1.85
296 297 2.402707 GCGCGCTAAAACCAAACTTTAC 59.597 45.455 26.67 0.00 0.00 2.01
297 298 2.975193 CGCGCTAAAACCAAACTTTACC 59.025 45.455 5.56 0.00 0.00 2.85
298 299 2.975193 GCGCTAAAACCAAACTTTACCG 59.025 45.455 0.00 0.00 0.00 4.02
299 300 2.975193 CGCTAAAACCAAACTTTACCGC 59.025 45.455 0.00 0.00 0.00 5.68
300 301 2.975193 GCTAAAACCAAACTTTACCGCG 59.025 45.455 0.00 0.00 0.00 6.46
301 302 1.842720 AAAACCAAACTTTACCGCGC 58.157 45.000 0.00 0.00 0.00 6.86
302 303 0.317186 AAACCAAACTTTACCGCGCG 60.317 50.000 25.67 25.67 0.00 6.86
303 304 2.120355 AACCAAACTTTACCGCGCGG 62.120 55.000 44.88 44.88 42.03 6.46
326 327 3.977244 CCTTTTGCCGCGCCTGTT 61.977 61.111 0.00 0.00 0.00 3.16
327 328 2.730604 CTTTTGCCGCGCCTGTTG 60.731 61.111 0.00 0.00 0.00 3.33
328 329 4.277593 TTTTGCCGCGCCTGTTGG 62.278 61.111 0.00 0.00 0.00 3.77
333 334 3.197790 CCGCGCCTGTTGGAGATG 61.198 66.667 0.00 0.00 34.95 2.90
334 335 3.869272 CGCGCCTGTTGGAGATGC 61.869 66.667 0.00 0.00 34.95 3.91
335 336 2.437359 GCGCCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 34.95 3.79
384 385 1.066143 CATCAAGCTAACCCCGTCAGT 60.066 52.381 0.00 0.00 0.00 3.41
395 396 1.004979 CCCCGTCAGTATTTCCCCAAA 59.995 52.381 0.00 0.00 0.00 3.28
427 444 1.760029 ACAAACCACCCTTTCGCAATT 59.240 42.857 0.00 0.00 0.00 2.32
447 464 2.407616 CATGTGCGAGGCATGCAG 59.592 61.111 21.36 11.27 44.21 4.41
455 472 0.033090 CGAGGCATGCAGCTCTATCA 59.967 55.000 21.36 0.00 44.79 2.15
500 517 1.160329 CGGATCGTTCCAGCCCATTC 61.160 60.000 12.88 0.00 42.74 2.67
564 598 4.640771 ACTAATGTGAGGGAGAAAAGCA 57.359 40.909 0.00 0.00 0.00 3.91
585 635 0.999406 CGATCCAACGCAACGATCTT 59.001 50.000 0.00 0.00 32.01 2.40
587 637 1.999735 GATCCAACGCAACGATCTTCA 59.000 47.619 0.00 0.00 31.59 3.02
588 638 1.872388 TCCAACGCAACGATCTTCAA 58.128 45.000 0.00 0.00 0.00 2.69
589 639 2.422597 TCCAACGCAACGATCTTCAAT 58.577 42.857 0.00 0.00 0.00 2.57
590 640 2.811431 TCCAACGCAACGATCTTCAATT 59.189 40.909 0.00 0.00 0.00 2.32
591 641 3.252215 TCCAACGCAACGATCTTCAATTT 59.748 39.130 0.00 0.00 0.00 1.82
592 642 3.603770 CCAACGCAACGATCTTCAATTTC 59.396 43.478 0.00 0.00 0.00 2.17
593 643 4.466828 CAACGCAACGATCTTCAATTTCT 58.533 39.130 0.00 0.00 0.00 2.52
594 644 4.749245 ACGCAACGATCTTCAATTTCTT 57.251 36.364 0.00 0.00 0.00 2.52
595 645 4.712763 ACGCAACGATCTTCAATTTCTTC 58.287 39.130 0.00 0.00 0.00 2.87
596 646 4.213270 ACGCAACGATCTTCAATTTCTTCA 59.787 37.500 0.00 0.00 0.00 3.02
597 647 5.106555 ACGCAACGATCTTCAATTTCTTCAT 60.107 36.000 0.00 0.00 0.00 2.57
616 666 2.669240 CTCCCTCCCGTTTCCACC 59.331 66.667 0.00 0.00 0.00 4.61
651 706 0.817013 GTGCACTCCTCTCCTCTCTG 59.183 60.000 10.32 0.00 0.00 3.35
907 968 4.924187 CGGCCCAACCACCCCAAA 62.924 66.667 0.00 0.00 39.03 3.28
908 969 2.203922 GGCCCAACCACCCCAAAT 60.204 61.111 0.00 0.00 38.86 2.32
909 970 2.290287 GGCCCAACCACCCCAAATC 61.290 63.158 0.00 0.00 38.86 2.17
910 971 2.290287 GCCCAACCACCCCAAATCC 61.290 63.158 0.00 0.00 0.00 3.01
911 972 1.612146 CCCAACCACCCCAAATCCC 60.612 63.158 0.00 0.00 0.00 3.85
912 973 1.981853 CCAACCACCCCAAATCCCG 60.982 63.158 0.00 0.00 0.00 5.14
913 974 2.283604 AACCACCCCAAATCCCGC 60.284 61.111 0.00 0.00 0.00 6.13
914 975 4.733542 ACCACCCCAAATCCCGCG 62.734 66.667 0.00 0.00 0.00 6.46
933 994 2.363665 CCCCCAAATCCCCAACCG 60.364 66.667 0.00 0.00 0.00 4.44
934 995 2.767352 CCCCAAATCCCCAACCGA 59.233 61.111 0.00 0.00 0.00 4.69
935 996 1.077625 CCCCAAATCCCCAACCGAA 59.922 57.895 0.00 0.00 0.00 4.30
936 997 0.543174 CCCCAAATCCCCAACCGAAA 60.543 55.000 0.00 0.00 0.00 3.46
937 998 0.606096 CCCAAATCCCCAACCGAAAC 59.394 55.000 0.00 0.00 0.00 2.78
938 999 0.606096 CCAAATCCCCAACCGAAACC 59.394 55.000 0.00 0.00 0.00 3.27
939 1000 0.242555 CAAATCCCCAACCGAAACCG 59.757 55.000 0.00 0.00 0.00 4.44
940 1001 1.529152 AAATCCCCAACCGAAACCGC 61.529 55.000 0.00 0.00 0.00 5.68
941 1002 2.700407 AATCCCCAACCGAAACCGCA 62.700 55.000 0.00 0.00 0.00 5.69
942 1003 3.666253 CCCCAACCGAAACCGCAC 61.666 66.667 0.00 0.00 0.00 5.34
943 1004 4.020378 CCCAACCGAAACCGCACG 62.020 66.667 0.00 0.00 0.00 5.34
944 1005 4.676586 CCAACCGAAACCGCACGC 62.677 66.667 0.00 0.00 0.00 5.34
945 1006 3.943034 CAACCGAAACCGCACGCA 61.943 61.111 0.00 0.00 0.00 5.24
946 1007 3.944233 AACCGAAACCGCACGCAC 61.944 61.111 0.00 0.00 0.00 5.34
947 1008 4.903010 ACCGAAACCGCACGCACT 62.903 61.111 0.00 0.00 0.00 4.40
948 1009 4.072088 CCGAAACCGCACGCACTC 62.072 66.667 0.00 0.00 0.00 3.51
949 1010 4.072088 CGAAACCGCACGCACTCC 62.072 66.667 0.00 0.00 0.00 3.85
950 1011 2.970324 GAAACCGCACGCACTCCA 60.970 61.111 0.00 0.00 0.00 3.86
951 1012 3.236618 GAAACCGCACGCACTCCAC 62.237 63.158 0.00 0.00 0.00 4.02
952 1013 3.750373 AAACCGCACGCACTCCACT 62.750 57.895 0.00 0.00 0.00 4.00
953 1014 4.664677 ACCGCACGCACTCCACTC 62.665 66.667 0.00 0.00 0.00 3.51
955 1016 4.662961 CGCACGCACTCCACTCCA 62.663 66.667 0.00 0.00 0.00 3.86
1176 1390 1.453379 CCTCCTCCTCTTCGCCGTA 60.453 63.158 0.00 0.00 0.00 4.02
1764 1987 2.514803 GTGAACCCCTATGTGCACTTT 58.485 47.619 19.41 8.24 40.94 2.66
1887 2110 2.743928 CAGGGCTTGTCTGACGGC 60.744 66.667 14.36 14.36 34.36 5.68
2037 2260 3.565902 TCAATACATTGTTCCACGCACAA 59.434 39.130 0.00 0.00 38.49 3.33
2400 2623 4.971125 GGGTATCGGCAGCCTCGC 62.971 72.222 10.54 2.23 33.12 5.03
2427 2650 2.681848 GTCATTGGAGATTGACAGGCAG 59.318 50.000 0.00 0.00 41.48 4.85
2493 2716 2.821366 CTGCCATCCGTGCACCTC 60.821 66.667 12.15 0.00 34.46 3.85
2921 3159 6.043411 GCTCCTAACTAGATTACAGTGTTGG 58.957 44.000 0.00 0.00 0.00 3.77
3226 6277 7.284820 AGTTAGGTCTGGTTACTAAAGCAAAA 58.715 34.615 0.00 0.00 42.24 2.44
3254 6307 4.033817 GCAACAGAAAAGAGATCATCTCCG 59.966 45.833 11.33 0.00 44.42 4.63
3282 6335 4.013728 TGTTTGCAAGTTCAACTACTGGT 58.986 39.130 0.00 0.00 0.00 4.00
3397 6450 2.040813 CCTGCCATCCTGCAATATAGGT 59.959 50.000 0.00 0.00 41.51 3.08
3410 6463 5.163652 TGCAATATAGGTCGTCCGATCTATG 60.164 44.000 25.24 15.34 45.20 2.23
3471 9645 0.346932 ATACCCACACCCCTCTCCAT 59.653 55.000 0.00 0.00 0.00 3.41
3488 9662 5.207354 TCTCCATATTTGCAAATAAGGCCA 58.793 37.500 33.70 24.18 38.79 5.36
3551 9725 4.100707 ACAAATGCATCTTGATGTTCCG 57.899 40.909 20.96 1.56 0.00 4.30
3572 9746 0.524816 GCAACGCATGAGCATCTTGG 60.525 55.000 0.00 0.00 40.31 3.61
3593 9767 9.162733 TCTTGGTAGTTATAACTAAATAGGGGG 57.837 37.037 23.66 10.81 42.66 5.40
3826 10000 2.481276 GCAAGCCGACAAGGAAAAACTT 60.481 45.455 0.00 0.00 45.00 2.66
3838 10012 7.489160 ACAAGGAAAAACTTTGGATAACTGAC 58.511 34.615 0.00 0.00 39.42 3.51
3949 10126 7.621428 AGGATTCACATTACTTTCTCATGTG 57.379 36.000 5.34 5.34 46.21 3.21
4046 10223 1.234615 TTAAGCAGGTCGTTGGCAGC 61.235 55.000 0.00 0.00 0.00 5.25
4262 10439 7.362056 CCTCAAAATTTTGATTCGGAAGCTCTA 60.362 37.037 28.86 6.55 45.26 2.43
4352 10529 3.004734 CACCTGCTGTTTTCCCAGTTAAG 59.995 47.826 0.00 0.00 34.84 1.85
4436 10613 9.144747 CTTCTGATGGAGTTGGTATAAATATCG 57.855 37.037 0.00 0.00 0.00 2.92
4502 10679 5.038033 CCAGAGTAGACAGCGATAGTTTTC 58.962 45.833 0.00 0.00 39.35 2.29
4635 10812 2.033141 TGCTGTCCTGCTGAAGGC 59.967 61.111 0.00 0.00 46.92 4.35
4662 10839 5.606348 AAGGATAGCTAAGACTTCACTGG 57.394 43.478 0.00 0.00 0.00 4.00
4751 10928 3.119101 ACTTGAGCAGTCTATTGTACCCG 60.119 47.826 0.00 0.00 0.00 5.28
4866 11043 7.997107 TGTTTGTGTTTGTCTAGTACTACTG 57.003 36.000 0.00 0.00 0.00 2.74
5058 11243 9.438291 CTATTTATGTTGTTTAGCAAAGGATCG 57.562 33.333 0.00 0.00 39.03 3.69
5102 11287 9.912634 AAACATACTACAAGATCCAACAAATTG 57.087 29.630 0.00 0.00 35.40 2.32
5143 11328 8.842358 ACAGAGATCCGTGATAAAACTTAAAA 57.158 30.769 0.00 0.00 0.00 1.52
5144 11329 8.936864 ACAGAGATCCGTGATAAAACTTAAAAG 58.063 33.333 0.00 0.00 0.00 2.27
5216 11401 5.664294 TTGCAACTTGATATTCCAGCATT 57.336 34.783 0.00 0.00 0.00 3.56
5217 11402 5.001237 TGCAACTTGATATTCCAGCATTG 57.999 39.130 0.00 0.00 0.00 2.82
5218 11403 4.705991 TGCAACTTGATATTCCAGCATTGA 59.294 37.500 0.00 0.00 0.00 2.57
5219 11404 5.039333 GCAACTTGATATTCCAGCATTGAC 58.961 41.667 0.00 0.00 0.00 3.18
5221 11406 4.210331 ACTTGATATTCCAGCATTGACCC 58.790 43.478 0.00 0.00 0.00 4.46
5222 11407 3.949586 TGATATTCCAGCATTGACCCA 57.050 42.857 0.00 0.00 0.00 4.51
5248 11433 9.480053 AGTTGATGAAATTAAAGACCAAACATG 57.520 29.630 0.00 0.00 0.00 3.21
5255 11440 9.180678 GAAATTAAAGACCAAACATGTACACAG 57.819 33.333 0.00 0.00 0.00 3.66
5295 11645 1.398692 TGTGAAAAGGTGTTGAGCCC 58.601 50.000 0.00 0.00 0.00 5.19
5302 11652 2.570181 GTGTTGAGCCCTGCATGC 59.430 61.111 11.82 11.82 0.00 4.06
5374 11734 6.429385 GGACTTGATGTCTCTTTGAATTCACT 59.571 38.462 7.89 0.00 44.74 3.41
5397 11757 7.116948 CACTAGAGTTTGTGTGGATTAAGACTG 59.883 40.741 0.00 0.00 0.00 3.51
5413 11773 9.543018 GATTAAGACTGGTTTCACTTAAAATCG 57.457 33.333 0.00 0.00 38.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.659089 TTCTTCGGGCTACTGCGGC 62.659 63.158 0.00 0.00 40.82 6.53
15 16 1.810030 GTTCTTCGGGCTACTGCGG 60.810 63.158 0.00 0.00 40.82 5.69
16 17 1.810030 GGTTCTTCGGGCTACTGCG 60.810 63.158 0.00 0.00 40.82 5.18
17 18 1.449778 GGGTTCTTCGGGCTACTGC 60.450 63.158 0.00 0.00 38.76 4.40
18 19 1.221021 GGGGTTCTTCGGGCTACTG 59.779 63.158 0.00 0.00 0.00 2.74
19 20 2.356780 CGGGGTTCTTCGGGCTACT 61.357 63.158 0.00 0.00 0.00 2.57
20 21 2.186125 CGGGGTTCTTCGGGCTAC 59.814 66.667 0.00 0.00 0.00 3.58
21 22 3.078836 CCGGGGTTCTTCGGGCTA 61.079 66.667 0.00 0.00 42.32 3.93
49 50 4.481112 CTTTCCGCGCCACCATGC 62.481 66.667 0.00 0.00 0.00 4.06
50 51 3.055719 ACTTTCCGCGCCACCATG 61.056 61.111 0.00 0.00 0.00 3.66
51 52 3.055719 CACTTTCCGCGCCACCAT 61.056 61.111 0.00 0.00 0.00 3.55
59 60 4.445545 CGCTTCGCCACTTTCCGC 62.446 66.667 0.00 0.00 0.00 5.54
60 61 3.788766 CCGCTTCGCCACTTTCCG 61.789 66.667 0.00 0.00 0.00 4.30
61 62 4.103103 GCCGCTTCGCCACTTTCC 62.103 66.667 0.00 0.00 0.00 3.13
62 63 4.445545 CGCCGCTTCGCCACTTTC 62.446 66.667 0.00 0.00 0.00 2.62
63 64 4.980805 TCGCCGCTTCGCCACTTT 62.981 61.111 0.00 0.00 0.00 2.66
93 94 4.821589 CTCCCCTCGCAACCTCGC 62.822 72.222 0.00 0.00 0.00 5.03
94 95 4.148825 CCTCCCCTCGCAACCTCG 62.149 72.222 0.00 0.00 0.00 4.63
95 96 3.787001 CCCTCCCCTCGCAACCTC 61.787 72.222 0.00 0.00 0.00 3.85
112 113 4.374702 CAGAACACAGCCACGCGC 62.375 66.667 5.73 0.00 37.98 6.86
113 114 2.967076 ACAGAACACAGCCACGCG 60.967 61.111 3.53 3.53 0.00 6.01
114 115 2.633657 CACAGAACACAGCCACGC 59.366 61.111 0.00 0.00 0.00 5.34
115 116 2.633657 GCACAGAACACAGCCACG 59.366 61.111 0.00 0.00 0.00 4.94
116 117 2.633657 CGCACAGAACACAGCCAC 59.366 61.111 0.00 0.00 0.00 5.01
117 118 3.279116 GCGCACAGAACACAGCCA 61.279 61.111 0.30 0.00 0.00 4.75
118 119 4.374702 CGCGCACAGAACACAGCC 62.375 66.667 8.75 0.00 0.00 4.85
119 120 3.640000 ACGCGCACAGAACACAGC 61.640 61.111 5.73 0.00 0.00 4.40
120 121 2.246397 CACGCGCACAGAACACAG 59.754 61.111 5.73 0.00 0.00 3.66
121 122 3.268603 CCACGCGCACAGAACACA 61.269 61.111 5.73 0.00 0.00 3.72
122 123 4.666532 GCCACGCGCACAGAACAC 62.667 66.667 5.73 0.00 37.47 3.32
136 137 2.933878 ATAAAATCCCGCGCTCGCCA 62.934 55.000 5.56 0.00 37.98 5.69
137 138 0.947180 TATAAAATCCCGCGCTCGCC 60.947 55.000 5.56 0.00 37.98 5.54
138 139 0.438830 CTATAAAATCCCGCGCTCGC 59.561 55.000 5.56 3.90 37.85 5.03
139 140 1.068474 CCTATAAAATCCCGCGCTCG 58.932 55.000 5.56 0.00 0.00 5.03
140 141 0.796927 GCCTATAAAATCCCGCGCTC 59.203 55.000 5.56 0.00 0.00 5.03
141 142 0.949105 CGCCTATAAAATCCCGCGCT 60.949 55.000 5.56 0.00 32.57 5.92
142 143 1.495951 CGCCTATAAAATCCCGCGC 59.504 57.895 0.00 0.00 32.57 6.86
143 144 1.495951 GCGCCTATAAAATCCCGCG 59.504 57.895 0.00 0.00 42.33 6.46
144 145 1.495951 CGCGCCTATAAAATCCCGC 59.504 57.895 0.00 0.00 38.23 6.13
145 146 1.495951 GCGCGCCTATAAAATCCCG 59.504 57.895 23.24 0.00 0.00 5.14
146 147 1.495951 CGCGCGCCTATAAAATCCC 59.504 57.895 27.72 0.00 0.00 3.85
147 148 1.154469 GCGCGCGCCTATAAAATCC 60.154 57.895 42.83 12.00 34.56 3.01
148 149 1.507096 CGCGCGCGCCTATAAAATC 60.507 57.895 44.64 17.46 37.98 2.17
149 150 1.492319 TTCGCGCGCGCCTATAAAAT 61.492 50.000 45.41 0.00 39.59 1.82
150 151 2.084763 CTTCGCGCGCGCCTATAAAA 62.085 55.000 45.41 30.82 39.59 1.52
151 152 2.582265 CTTCGCGCGCGCCTATAAA 61.582 57.895 45.41 31.52 39.59 1.40
152 153 3.028019 CTTCGCGCGCGCCTATAA 61.028 61.111 45.41 32.23 39.59 0.98
165 166 1.810030 GGTAGACTTGGCGGCTTCG 60.810 63.158 11.43 0.50 0.00 3.79
166 167 1.810030 CGGTAGACTTGGCGGCTTC 60.810 63.158 11.43 4.04 0.00 3.86
167 168 2.264794 CGGTAGACTTGGCGGCTT 59.735 61.111 11.43 0.00 0.00 4.35
168 169 4.452733 GCGGTAGACTTGGCGGCT 62.453 66.667 11.43 0.00 0.00 5.52
226 227 3.484547 GGGAACTTACCGTGCGCG 61.485 66.667 13.88 13.88 37.95 6.86
227 228 3.484547 CGGGAACTTACCGTGCGC 61.485 66.667 4.03 0.00 46.03 6.09
233 234 2.435410 CGGTGGCGGGAACTTACC 60.435 66.667 0.00 0.00 0.00 2.85
234 235 3.122971 GCGGTGGCGGGAACTTAC 61.123 66.667 0.00 0.00 0.00 2.34
235 236 3.315949 AGCGGTGGCGGGAACTTA 61.316 61.111 0.00 0.00 46.35 2.24
272 273 3.882835 TTTGGTTTTAGCGCGCGCC 62.883 57.895 46.98 32.13 43.17 6.53
273 274 2.427740 TTTGGTTTTAGCGCGCGC 60.428 55.556 45.10 45.10 42.33 6.86
274 275 0.659123 AAGTTTGGTTTTAGCGCGCG 60.659 50.000 28.44 28.44 0.00 6.86
275 276 1.483316 AAAGTTTGGTTTTAGCGCGC 58.517 45.000 26.66 26.66 0.00 6.86
276 277 2.975193 GGTAAAGTTTGGTTTTAGCGCG 59.025 45.455 0.00 0.00 31.42 6.86
279 280 2.975193 CGCGGTAAAGTTTGGTTTTAGC 59.025 45.455 0.00 0.00 35.97 3.09
280 281 2.975193 GCGCGGTAAAGTTTGGTTTTAG 59.025 45.455 8.83 0.00 0.00 1.85
281 282 2.601741 CGCGCGGTAAAGTTTGGTTTTA 60.602 45.455 24.84 0.00 0.00 1.52
282 283 1.842720 GCGCGGTAAAGTTTGGTTTT 58.157 45.000 8.83 0.00 0.00 2.43
283 284 0.317186 CGCGCGGTAAAGTTTGGTTT 60.317 50.000 24.84 0.00 0.00 3.27
284 285 1.280444 CGCGCGGTAAAGTTTGGTT 59.720 52.632 24.84 0.00 0.00 3.67
285 286 2.609759 CCGCGCGGTAAAGTTTGGT 61.610 57.895 39.71 0.00 0.00 3.67
286 287 2.174835 CCGCGCGGTAAAGTTTGG 59.825 61.111 39.71 11.06 0.00 3.28
287 288 2.174835 CCCGCGCGGTAAAGTTTG 59.825 61.111 43.12 24.12 0.00 2.93
288 289 3.729698 GCCCGCGCGGTAAAGTTT 61.730 61.111 43.12 0.00 0.00 2.66
309 310 3.977244 AACAGGCGCGGCAAAAGG 61.977 61.111 34.94 19.28 0.00 3.11
310 311 2.730604 CAACAGGCGCGGCAAAAG 60.731 61.111 34.94 22.03 0.00 2.27
311 312 4.277593 CCAACAGGCGCGGCAAAA 62.278 61.111 34.94 0.00 0.00 2.44
316 317 3.197790 CATCTCCAACAGGCGCGG 61.198 66.667 8.83 0.00 0.00 6.46
317 318 3.869272 GCATCTCCAACAGGCGCG 61.869 66.667 0.00 0.00 0.00 6.86
318 319 0.744414 TAAGCATCTCCAACAGGCGC 60.744 55.000 0.00 0.00 0.00 6.53
319 320 1.737838 TTAAGCATCTCCAACAGGCG 58.262 50.000 0.00 0.00 0.00 5.52
320 321 4.519540 TTTTTAAGCATCTCCAACAGGC 57.480 40.909 0.00 0.00 0.00 4.85
343 344 4.816126 TGGGCCTATGATCAACTACTACT 58.184 43.478 4.53 0.00 0.00 2.57
345 346 5.402630 TGATGGGCCTATGATCAACTACTA 58.597 41.667 6.22 0.00 0.00 1.82
347 348 4.623932 TGATGGGCCTATGATCAACTAC 57.376 45.455 6.22 0.00 0.00 2.73
351 352 2.444388 AGCTTGATGGGCCTATGATCAA 59.556 45.455 6.22 14.25 35.37 2.57
356 357 2.508526 GGTTAGCTTGATGGGCCTATG 58.491 52.381 6.22 0.00 0.00 2.23
384 385 5.732331 AGATCTGGATGTTTGGGGAAATA 57.268 39.130 0.00 0.00 0.00 1.40
395 396 3.054361 GGGTGGTTTGTAGATCTGGATGT 60.054 47.826 5.18 0.00 0.00 3.06
455 472 7.550196 GCATCACCATTCATTAAGGAATTGTTT 59.450 33.333 14.73 5.52 35.37 2.83
538 556 7.336931 TGCTTTTCTCCCTCACATTAGTTTATC 59.663 37.037 0.00 0.00 0.00 1.75
548 580 0.250295 CGGTGCTTTTCTCCCTCACA 60.250 55.000 0.00 0.00 0.00 3.58
552 586 0.253327 GGATCGGTGCTTTTCTCCCT 59.747 55.000 0.00 0.00 0.00 4.20
564 598 1.079405 ATCGTTGCGTTGGATCGGT 60.079 52.632 0.00 0.00 0.00 4.69
585 635 3.203040 GGGAGGGAGGATGAAGAAATTGA 59.797 47.826 0.00 0.00 0.00 2.57
587 637 2.173569 CGGGAGGGAGGATGAAGAAATT 59.826 50.000 0.00 0.00 0.00 1.82
588 638 1.771255 CGGGAGGGAGGATGAAGAAAT 59.229 52.381 0.00 0.00 0.00 2.17
589 639 1.204146 CGGGAGGGAGGATGAAGAAA 58.796 55.000 0.00 0.00 0.00 2.52
590 640 0.042731 ACGGGAGGGAGGATGAAGAA 59.957 55.000 0.00 0.00 0.00 2.52
591 641 0.042731 AACGGGAGGGAGGATGAAGA 59.957 55.000 0.00 0.00 0.00 2.87
592 642 0.912486 AAACGGGAGGGAGGATGAAG 59.088 55.000 0.00 0.00 0.00 3.02
593 643 0.909623 GAAACGGGAGGGAGGATGAA 59.090 55.000 0.00 0.00 0.00 2.57
594 644 0.981277 GGAAACGGGAGGGAGGATGA 60.981 60.000 0.00 0.00 0.00 2.92
595 645 1.271840 TGGAAACGGGAGGGAGGATG 61.272 60.000 0.00 0.00 0.00 3.51
596 646 1.082206 TGGAAACGGGAGGGAGGAT 59.918 57.895 0.00 0.00 0.00 3.24
597 647 1.916777 GTGGAAACGGGAGGGAGGA 60.917 63.158 0.00 0.00 0.00 3.71
635 687 2.239654 AGAGACAGAGAGGAGAGGAGTG 59.760 54.545 0.00 0.00 0.00 3.51
636 688 2.239654 CAGAGACAGAGAGGAGAGGAGT 59.760 54.545 0.00 0.00 0.00 3.85
637 689 2.421952 CCAGAGACAGAGAGGAGAGGAG 60.422 59.091 0.00 0.00 0.00 3.69
638 690 1.563879 CCAGAGACAGAGAGGAGAGGA 59.436 57.143 0.00 0.00 0.00 3.71
640 692 1.392589 GCCAGAGACAGAGAGGAGAG 58.607 60.000 0.00 0.00 0.00 3.20
641 693 0.033601 GGCCAGAGACAGAGAGGAGA 60.034 60.000 0.00 0.00 0.00 3.71
651 706 2.185608 GGAGAAGCGGCCAGAGAC 59.814 66.667 2.24 0.00 0.00 3.36
916 977 2.363665 CGGTTGGGGATTTGGGGG 60.364 66.667 0.00 0.00 0.00 5.40
917 978 0.543174 TTTCGGTTGGGGATTTGGGG 60.543 55.000 0.00 0.00 0.00 4.96
918 979 0.606096 GTTTCGGTTGGGGATTTGGG 59.394 55.000 0.00 0.00 0.00 4.12
919 980 0.606096 GGTTTCGGTTGGGGATTTGG 59.394 55.000 0.00 0.00 0.00 3.28
920 981 0.242555 CGGTTTCGGTTGGGGATTTG 59.757 55.000 0.00 0.00 0.00 2.32
921 982 1.529152 GCGGTTTCGGTTGGGGATTT 61.529 55.000 0.00 0.00 36.79 2.17
922 983 1.974875 GCGGTTTCGGTTGGGGATT 60.975 57.895 0.00 0.00 36.79 3.01
923 984 2.360726 GCGGTTTCGGTTGGGGAT 60.361 61.111 0.00 0.00 36.79 3.85
924 985 3.875023 TGCGGTTTCGGTTGGGGA 61.875 61.111 0.00 0.00 36.79 4.81
925 986 3.666253 GTGCGGTTTCGGTTGGGG 61.666 66.667 0.00 0.00 36.79 4.96
926 987 4.020378 CGTGCGGTTTCGGTTGGG 62.020 66.667 0.00 0.00 36.79 4.12
927 988 4.676586 GCGTGCGGTTTCGGTTGG 62.677 66.667 0.00 0.00 36.79 3.77
928 989 3.943034 TGCGTGCGGTTTCGGTTG 61.943 61.111 0.00 0.00 36.79 3.77
929 990 3.944233 GTGCGTGCGGTTTCGGTT 61.944 61.111 0.00 0.00 36.79 4.44
930 991 4.903010 AGTGCGTGCGGTTTCGGT 62.903 61.111 0.00 0.00 36.79 4.69
931 992 4.072088 GAGTGCGTGCGGTTTCGG 62.072 66.667 0.00 0.00 36.79 4.30
932 993 4.072088 GGAGTGCGTGCGGTTTCG 62.072 66.667 0.00 0.00 39.81 3.46
933 994 2.970324 TGGAGTGCGTGCGGTTTC 60.970 61.111 0.00 0.00 0.00 2.78
934 995 3.276846 GTGGAGTGCGTGCGGTTT 61.277 61.111 0.00 0.00 0.00 3.27
935 996 4.235762 AGTGGAGTGCGTGCGGTT 62.236 61.111 0.00 0.00 0.00 4.44
936 997 4.664677 GAGTGGAGTGCGTGCGGT 62.665 66.667 0.00 0.00 0.00 5.68
938 999 4.662961 TGGAGTGGAGTGCGTGCG 62.663 66.667 0.00 0.00 0.00 5.34
939 1000 3.044305 GTGGAGTGGAGTGCGTGC 61.044 66.667 0.00 0.00 0.00 5.34
940 1001 2.357517 GGTGGAGTGGAGTGCGTG 60.358 66.667 0.00 0.00 0.00 5.34
941 1002 3.626924 GGGTGGAGTGGAGTGCGT 61.627 66.667 0.00 0.00 0.00 5.24
942 1003 4.394712 GGGGTGGAGTGGAGTGCG 62.395 72.222 0.00 0.00 0.00 5.34
943 1004 4.394712 CGGGGTGGAGTGGAGTGC 62.395 72.222 0.00 0.00 0.00 4.40
944 1005 4.394712 GCGGGGTGGAGTGGAGTG 62.395 72.222 0.00 0.00 0.00 3.51
954 1015 4.489771 GATCTGGGTGGCGGGGTG 62.490 72.222 0.00 0.00 0.00 4.61
1647 1870 0.855349 CGAAATGCTTCCCGAGATCG 59.145 55.000 0.00 0.00 39.44 3.69
1839 2062 1.522580 GCGGCCACTGAAGATCTCC 60.523 63.158 2.24 0.00 0.00 3.71
1887 2110 2.484062 GGCATCCACATCCGGCAAG 61.484 63.158 0.00 0.00 0.00 4.01
2037 2260 1.210204 TCATCAGGCCCCAGAAAGCT 61.210 55.000 0.00 0.00 0.00 3.74
2493 2716 0.894141 TGCCAATTTCATCAACCCCG 59.106 50.000 0.00 0.00 0.00 5.73
2625 2848 6.574350 GGTCTTGAATATCCGTCCATATAGG 58.426 44.000 0.00 0.00 39.47 2.57
2776 3006 9.398538 TCATATCAAGTGATGATCATGTTTTGA 57.601 29.630 14.30 17.74 45.91 2.69
2790 3020 8.283699 TGCAGATTGATTTTCATATCAAGTGA 57.716 30.769 12.24 0.00 45.00 3.41
2894 3132 5.163499 ACACTGTAATCTAGTTAGGAGCTGC 60.163 44.000 0.00 0.00 0.00 5.25
2980 3654 9.981114 AAATGTGTTTATTCTAAAAGAACCTGG 57.019 29.630 0.00 0.00 37.00 4.45
3128 6179 6.590656 AGGAAATAAGATGTTATGGGTGGA 57.409 37.500 0.00 0.00 0.00 4.02
3226 6277 6.433404 AGATGATCTCTTTTCTGTTGCATTGT 59.567 34.615 0.00 0.00 0.00 2.71
3254 6307 7.166473 CAGTAGTTGAACTTGCAAACAGAAATC 59.834 37.037 1.97 0.00 0.00 2.17
3282 6335 7.277396 CCCATCGGTAAGGTTATCTTTTAAGA 58.723 38.462 0.00 0.00 39.78 2.10
3336 6389 8.660373 CCAACTCTGCTTTTTATAAGAGTAGTG 58.340 37.037 4.72 12.36 46.64 2.74
3337 6390 8.376270 ACCAACTCTGCTTTTTATAAGAGTAGT 58.624 33.333 4.72 3.71 46.64 2.73
3338 6391 8.660373 CACCAACTCTGCTTTTTATAAGAGTAG 58.340 37.037 4.72 6.39 46.64 2.57
3339 6392 8.372459 TCACCAACTCTGCTTTTTATAAGAGTA 58.628 33.333 4.72 0.00 46.64 2.59
3341 6394 7.672983 TCACCAACTCTGCTTTTTATAAGAG 57.327 36.000 0.00 0.00 41.59 2.85
3353 6406 1.741706 CACCATCATCACCAACTCTGC 59.258 52.381 0.00 0.00 0.00 4.26
3410 6463 3.447944 AGTTTCCTTCCTATCCGTCAGAC 59.552 47.826 0.00 0.00 0.00 3.51
3471 9645 4.555689 AGGGATGGCCTTATTTGCAAATA 58.444 39.130 24.63 24.63 0.00 1.40
3488 9662 3.118223 GGAGAAAAGGATGAACGAGGGAT 60.118 47.826 0.00 0.00 0.00 3.85
3551 9725 0.169672 AAGATGCTCATGCGTTGCAC 59.830 50.000 5.61 1.79 43.04 4.57
3593 9767 9.220767 AGAAGGTAAGTCAAGTCAATTTCATAC 57.779 33.333 0.00 0.00 0.00 2.39
3826 10000 6.833041 TCTACAAACCTTGTCAGTTATCCAA 58.167 36.000 0.00 0.00 44.12 3.53
3838 10012 4.809426 GGTGGATACGATCTACAAACCTTG 59.191 45.833 11.37 0.00 41.93 3.61
3949 10126 1.134907 CCCAAGAATGTGCAATCTGCC 60.135 52.381 0.00 0.00 44.23 4.85
4046 10223 2.619074 GGACTGGAAATGAACAGGGGAG 60.619 54.545 0.00 0.00 39.00 4.30
4262 10439 1.947456 GTCTTGAAAACTGTTCCGGCT 59.053 47.619 0.00 0.00 0.00 5.52
4352 10529 5.801350 TGAAATCAATCTCGTTCATCACC 57.199 39.130 0.00 0.00 0.00 4.02
4436 10613 7.698836 ATGTTTGCATTTCAACTACAAGAAC 57.301 32.000 0.00 0.00 31.45 3.01
4502 10679 3.555966 ACAGAGAAACCCCTGAAAACTG 58.444 45.455 0.00 0.00 34.65 3.16
4635 10812 6.876257 AGTGAAGTCTTAGCTATCCTTTGTTG 59.124 38.462 0.00 0.00 0.00 3.33
4638 10815 5.814705 CCAGTGAAGTCTTAGCTATCCTTTG 59.185 44.000 0.00 0.00 0.00 2.77
4662 10839 2.182030 CCACGTCGAGGCTCTTCC 59.818 66.667 13.50 0.00 0.00 3.46
4751 10928 6.347888 CCTGATTTTCATTTGCCAATGTTGAC 60.348 38.462 10.07 1.92 40.78 3.18
4866 11043 1.204467 CTCTGTCTCAGTCCAGAAGGC 59.796 57.143 0.00 0.00 37.27 4.35
4896 11081 5.177327 CACCAAGACCACAAAATTATGCAAC 59.823 40.000 0.00 0.00 0.00 4.17
4902 11087 4.404073 ACAAGCACCAAGACCACAAAATTA 59.596 37.500 0.00 0.00 0.00 1.40
5071 11256 8.380099 TGTTGGATCTTGTAGTATGTTTAGGTT 58.620 33.333 0.00 0.00 0.00 3.50
5087 11272 8.614346 CATGTTTGTTTCAATTTGTTGGATCTT 58.386 29.630 0.00 0.00 0.00 2.40
5102 11287 7.025963 GGATCTCTGTCATTCATGTTTGTTTC 58.974 38.462 0.00 0.00 0.00 2.78
5143 11328 8.437575 TCAAAGAACCTTAATAGGACTTGAACT 58.562 33.333 0.00 0.00 45.05 3.01
5144 11329 8.617290 TCAAAGAACCTTAATAGGACTTGAAC 57.383 34.615 0.00 0.00 45.05 3.18
5146 11331 9.807921 ATTTCAAAGAACCTTAATAGGACTTGA 57.192 29.630 0.00 0.00 45.05 3.02
5151 11336 9.595823 CGTAGATTTCAAAGAACCTTAATAGGA 57.404 33.333 0.00 0.00 45.05 2.94
5174 11359 4.806330 CAAAAGGTGAAGCTAGAGACGTA 58.194 43.478 0.00 0.00 0.00 3.57
5216 11401 6.208599 GGTCTTTAATTTCATCAACTGGGTCA 59.791 38.462 0.00 0.00 0.00 4.02
5217 11402 6.208599 TGGTCTTTAATTTCATCAACTGGGTC 59.791 38.462 0.00 0.00 0.00 4.46
5218 11403 6.074648 TGGTCTTTAATTTCATCAACTGGGT 58.925 36.000 0.00 0.00 0.00 4.51
5219 11404 6.588719 TGGTCTTTAATTTCATCAACTGGG 57.411 37.500 0.00 0.00 0.00 4.45
5221 11406 8.870160 TGTTTGGTCTTTAATTTCATCAACTG 57.130 30.769 0.00 0.00 0.00 3.16
5222 11407 9.480053 CATGTTTGGTCTTTAATTTCATCAACT 57.520 29.630 0.00 0.00 0.00 3.16
5248 11433 2.820787 ACTGCTAGTCCAGTCTGTGTAC 59.179 50.000 0.00 0.00 42.10 2.90
5255 11440 3.669251 ACTTTCACTGCTAGTCCAGTC 57.331 47.619 0.46 0.00 43.85 3.51
5295 11645 3.285484 AGGTTTCCAGAATAGCATGCAG 58.715 45.455 21.98 1.97 0.00 4.41
5374 11734 6.042781 ACCAGTCTTAATCCACACAAACTCTA 59.957 38.462 0.00 0.00 0.00 2.43
5397 11757 8.791355 ATTGTACAACGATTTTAAGTGAAACC 57.209 30.769 11.22 0.00 37.80 3.27


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

AutoCloner maintained by Alex Coulton.