Multiple sequence alignment - TraesCS6A01G056700

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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 TraesCS6A01G056700 chr6A 100.000 3435 0 0 1 3435 29807851 29804417 0.000000e+00 6344.0
1 TraesCS6A01G056700 chr6A 90.529 813 46 12 1492 2300 29755278 29756063 0.000000e+00 1046.0
2 TraesCS6A01G056700 chr6A 100.000 180 0 0 3865 4044 29803987 29803808 2.330000e-87 333.0
3 TraesCS6A01G056700 chr6A 83.019 371 29 13 911 1273 29716556 29716900 5.080000e-79 305.0
4 TraesCS6A01G056700 chr6A 92.130 216 15 1 1283 1498 29737748 29737961 1.830000e-78 303.0
5 TraesCS6A01G056700 chr6A 89.103 156 13 3 594 747 29713336 29713489 1.480000e-44 191.0
6 TraesCS6A01G056700 chr6A 88.298 94 10 1 74 167 39461227 39461135 1.190000e-20 111.0
7 TraesCS6A01G056700 chr6D 88.022 2538 181 58 876 3334 28153769 28156262 0.000000e+00 2889.0
8 TraesCS6A01G056700 chr6D 87.652 1320 123 18 1124 2425 28266067 28264770 0.000000e+00 1498.0
9 TraesCS6A01G056700 chr6D 82.266 406 47 11 173 556 28268025 28267623 1.080000e-85 327.0
10 TraesCS6A01G056700 chr6D 91.667 156 10 3 572 724 28144144 28144299 3.170000e-51 213.0
11 TraesCS6A01G056700 chr6D 96.117 103 4 0 3333 3435 376104266 376104368 6.950000e-38 169.0
12 TraesCS6A01G056700 chr6D 92.647 68 4 1 797 864 28153721 28153787 3.330000e-16 97.1
13 TraesCS6A01G056700 chr6D 96.000 50 1 1 712 760 28144319 28144368 3.350000e-11 80.5
14 TraesCS6A01G056700 chr6D 100.000 29 0 0 775 803 28153633 28153661 2.000000e-03 54.7
15 TraesCS6A01G056700 chr6B 87.041 2585 191 69 845 3334 52138293 52135758 0.000000e+00 2785.0
16 TraesCS6A01G056700 chr6B 88.710 2108 141 36 901 2968 52075569 52077619 0.000000e+00 2484.0
17 TraesCS6A01G056700 chr6B 93.846 325 18 2 3014 3337 52077622 52077945 4.700000e-134 488.0
18 TraesCS6A01G056700 chr6B 88.936 235 23 2 572 803 52030074 52030308 1.840000e-73 287.0
19 TraesCS6A01G056700 chr6B 79.287 449 46 17 170 573 52061488 52061934 1.850000e-68 270.0
20 TraesCS6A01G056700 chr6B 86.383 235 27 2 339 573 52145614 52145385 6.710000e-63 252.0
21 TraesCS6A01G056700 chr6B 82.645 242 14 6 617 847 52141001 52140777 5.340000e-44 189.0
22 TraesCS6A01G056700 chr6B 79.439 214 40 3 363 573 52029826 52030038 9.060000e-32 148.0
23 TraesCS6A01G056700 chr6B 97.333 75 2 0 3865 3939 52077994 52078068 1.180000e-25 128.0
24 TraesCS6A01G056700 chr6B 93.333 75 5 0 3865 3939 52116295 52116221 1.190000e-20 111.0
25 TraesCS6A01G056700 chr6B 91.781 73 6 0 3867 3939 52116778 52116706 7.150000e-18 102.0
26 TraesCS6A01G056700 chr6B 79.310 145 19 8 607 747 52062013 52062150 1.550000e-14 91.6
27 TraesCS6A01G056700 chr6B 95.833 48 2 0 2 49 52146451 52146404 1.210000e-10 78.7
28 TraesCS6A01G056700 chr7B 97.087 103 3 0 3333 3435 559142307 559142205 1.490000e-39 174.0
29 TraesCS6A01G056700 chr5A 97.980 99 2 0 3337 3435 26132540 26132638 5.370000e-39 172.0
30 TraesCS6A01G056700 chr5A 88.172 93 10 1 74 166 157479163 157479254 4.270000e-20 110.0
31 TraesCS6A01G056700 chr1D 97.059 102 3 0 3334 3435 386156832 386156731 5.370000e-39 172.0
32 TraesCS6A01G056700 chr7A 97.030 101 3 0 3335 3435 488587525 488587425 1.930000e-38 171.0
33 TraesCS6A01G056700 chr5B 96.190 105 3 1 3332 3435 515669451 515669555 1.930000e-38 171.0
34 TraesCS6A01G056700 chr4A 96.154 104 4 0 3332 3435 90353258 90353361 1.930000e-38 171.0
35 TraesCS6A01G056700 chr2A 96.154 104 4 0 3332 3435 78333822 78333719 1.930000e-38 171.0
36 TraesCS6A01G056700 chr2A 88.421 95 11 0 73 167 569915636 569915730 9.180000e-22 115.0
37 TraesCS6A01G056700 chr3D 90.244 123 9 3 3315 3435 263778139 263778260 1.500000e-34 158.0
38 TraesCS6A01G056700 chr3D 88.172 93 11 0 73 165 601004375 601004467 1.190000e-20 111.0
39 TraesCS6A01G056700 chr3D 87.234 94 12 0 74 167 49477788 49477881 1.540000e-19 108.0
40 TraesCS6A01G056700 chr5D 91.489 94 7 1 74 166 296366714 296366807 1.180000e-25 128.0
41 TraesCS6A01G056700 chr5D 89.362 94 4 4 74 166 386645386 386645474 3.300000e-21 113.0
42 TraesCS6A01G056700 chr7D 88.172 93 11 0 74 166 632637750 632637842 1.190000e-20 111.0
43 TraesCS6A01G056700 chr1B 89.655 87 9 0 80 166 443495909 443495823 1.190000e-20 111.0


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 TraesCS6A01G056700 chr6A 29803808 29807851 4043 True 3338.500000 6344 100.000000 1 4044 2 chr6A.!!$R2 4043
1 TraesCS6A01G056700 chr6A 29755278 29756063 785 False 1046.000000 1046 90.529000 1492 2300 1 chr6A.!!$F2 808
2 TraesCS6A01G056700 chr6A 29713336 29716900 3564 False 248.000000 305 86.061000 594 1273 2 chr6A.!!$F3 679
3 TraesCS6A01G056700 chr6D 28153633 28156262 2629 False 1013.600000 2889 93.556333 775 3334 3 chr6D.!!$F3 2559
4 TraesCS6A01G056700 chr6D 28264770 28268025 3255 True 912.500000 1498 84.959000 173 2425 2 chr6D.!!$R1 2252
5 TraesCS6A01G056700 chr6B 52135758 52141001 5243 True 1487.000000 2785 84.843000 617 3334 2 chr6B.!!$R2 2717
6 TraesCS6A01G056700 chr6B 52075569 52078068 2499 False 1033.333333 2484 93.296333 901 3939 3 chr6B.!!$F3 3038

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
205 206 0.108396 TGCTCACACCTTGCTAAGCA 59.892 50.0 0.00 0.0 37.41 3.91 F
1477 7480 0.175073 GCGGGTTCTACGTCCTGAAT 59.825 55.0 4.08 0.0 32.26 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 7613 0.112412 AAATGCTTCCCGGGTTGTCT 59.888 50.000 22.86 0.5 0.00 3.41 R
3404 9515 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.0 39.69 3.06 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
18 19 3.520623 GGGGTGGCTCATAATTGCT 57.479 52.632 0.00 0.00 0.00 3.91
19 20 1.322442 GGGGTGGCTCATAATTGCTC 58.678 55.000 0.00 0.00 0.00 4.26
20 21 0.947244 GGGTGGCTCATAATTGCTCG 59.053 55.000 0.00 0.00 0.00 5.03
21 22 0.947244 GGTGGCTCATAATTGCTCGG 59.053 55.000 0.00 0.00 0.00 4.63
22 23 0.947244 GTGGCTCATAATTGCTCGGG 59.053 55.000 0.00 0.00 0.00 5.14
23 24 0.546122 TGGCTCATAATTGCTCGGGT 59.454 50.000 0.00 0.00 0.00 5.28
24 25 0.947244 GGCTCATAATTGCTCGGGTG 59.053 55.000 0.00 0.00 0.00 4.61
25 26 0.308993 GCTCATAATTGCTCGGGTGC 59.691 55.000 0.00 0.00 0.00 5.01
26 27 1.959042 CTCATAATTGCTCGGGTGCT 58.041 50.000 0.00 0.00 0.00 4.40
27 28 2.292267 CTCATAATTGCTCGGGTGCTT 58.708 47.619 0.00 0.00 0.00 3.91
28 29 2.016318 TCATAATTGCTCGGGTGCTTG 58.984 47.619 0.00 0.00 0.00 4.01
29 30 1.745087 CATAATTGCTCGGGTGCTTGT 59.255 47.619 0.00 0.00 0.00 3.16
30 31 1.164411 TAATTGCTCGGGTGCTTGTG 58.836 50.000 0.00 0.00 0.00 3.33
31 32 2.146073 AATTGCTCGGGTGCTTGTGC 62.146 55.000 0.00 0.00 40.20 4.57
34 35 2.662596 CTCGGGTGCTTGTGCCTA 59.337 61.111 0.00 0.00 38.71 3.93
35 36 1.221840 CTCGGGTGCTTGTGCCTAT 59.778 57.895 0.00 0.00 38.71 2.57
36 37 1.078497 TCGGGTGCTTGTGCCTATG 60.078 57.895 0.00 0.00 38.71 2.23
37 38 2.764314 CGGGTGCTTGTGCCTATGC 61.764 63.158 0.00 0.00 38.71 3.14
53 54 7.830940 TGCCTATGCAATTTGTCTTAATTTG 57.169 32.000 0.00 0.00 46.66 2.32
54 55 7.385267 TGCCTATGCAATTTGTCTTAATTTGT 58.615 30.769 0.00 0.00 46.66 2.83
55 56 7.545265 TGCCTATGCAATTTGTCTTAATTTGTC 59.455 33.333 0.00 0.00 46.66 3.18
56 57 7.761249 GCCTATGCAATTTGTCTTAATTTGTCT 59.239 33.333 0.00 0.00 37.47 3.41
57 58 9.643693 CCTATGCAATTTGTCTTAATTTGTCTT 57.356 29.630 0.00 0.00 0.00 3.01
85 86 9.562583 GTATATTCTTAGCTTCTACGAATCTGG 57.437 37.037 8.29 0.00 0.00 3.86
86 87 6.716934 ATTCTTAGCTTCTACGAATCTGGA 57.283 37.500 0.00 0.00 0.00 3.86
87 88 6.716934 TTCTTAGCTTCTACGAATCTGGAT 57.283 37.500 0.00 0.00 0.00 3.41
88 89 6.078202 TCTTAGCTTCTACGAATCTGGATG 57.922 41.667 0.00 0.00 0.00 3.51
89 90 5.594725 TCTTAGCTTCTACGAATCTGGATGT 59.405 40.000 0.00 0.00 0.00 3.06
90 91 6.771267 TCTTAGCTTCTACGAATCTGGATGTA 59.229 38.462 0.00 0.00 0.00 2.29
91 92 5.854010 AGCTTCTACGAATCTGGATGTAA 57.146 39.130 0.00 0.00 0.00 2.41
92 93 6.412362 AGCTTCTACGAATCTGGATGTAAT 57.588 37.500 0.00 0.00 0.00 1.89
93 94 6.821388 AGCTTCTACGAATCTGGATGTAATT 58.179 36.000 0.00 0.00 0.00 1.40
94 95 7.275920 AGCTTCTACGAATCTGGATGTAATTT 58.724 34.615 0.00 0.00 0.00 1.82
95 96 7.770897 AGCTTCTACGAATCTGGATGTAATTTT 59.229 33.333 0.00 0.00 0.00 1.82
96 97 8.398665 GCTTCTACGAATCTGGATGTAATTTTT 58.601 33.333 0.00 0.00 0.00 1.94
131 132 9.508642 TGGTGTTCATTATACTGTAATGTTTGA 57.491 29.630 5.67 0.00 36.56 2.69
193 194 4.026052 TGAATAGGATCACTCTGCTCACA 58.974 43.478 0.00 0.00 0.00 3.58
196 197 0.901124 GGATCACTCTGCTCACACCT 59.099 55.000 0.00 0.00 0.00 4.00
205 206 0.108396 TGCTCACACCTTGCTAAGCA 59.892 50.000 0.00 0.00 37.41 3.91
206 207 0.519077 GCTCACACCTTGCTAAGCAC 59.481 55.000 0.00 0.00 38.71 4.40
212 213 1.375908 CCTTGCTAAGCACGAGCCA 60.376 57.895 0.00 0.00 43.56 4.75
217 218 1.591703 CTAAGCACGAGCCACCTCA 59.408 57.895 0.00 0.00 43.56 3.86
244 245 4.742201 CCCCGCACTCCTCACACG 62.742 72.222 0.00 0.00 0.00 4.49
248 249 3.106407 GCACTCCTCACACGCGTC 61.106 66.667 9.86 0.00 0.00 5.19
255 256 2.596338 TCACACGCGTCCTCCTCA 60.596 61.111 9.86 0.00 0.00 3.86
260 261 1.025113 CACGCGTCCTCCTCACTAGA 61.025 60.000 9.86 0.00 0.00 2.43
261 262 1.025647 ACGCGTCCTCCTCACTAGAC 61.026 60.000 5.58 0.00 0.00 2.59
268 269 2.110188 TCCTCCTCACTAGACTTGTGGT 59.890 50.000 15.59 0.00 36.21 4.16
285 286 0.604243 GGTACCATTGCACCGTCACA 60.604 55.000 7.15 0.00 0.00 3.58
286 287 0.515564 GTACCATTGCACCGTCACAC 59.484 55.000 0.00 0.00 0.00 3.82
294 295 1.812093 CACCGTCACACACCAACGT 60.812 57.895 0.00 0.00 34.71 3.99
303 304 2.326550 CACCAACGTGTCGCCAAC 59.673 61.111 0.00 0.00 35.10 3.77
306 307 3.656045 CAACGTGTCGCCAACCCC 61.656 66.667 0.00 0.00 0.00 4.95
327 331 2.755469 CCCGCCTTCCAATGTGGG 60.755 66.667 0.00 0.00 45.27 4.61
331 335 2.444696 CCTTCCAATGTGGGCCCA 59.555 61.111 24.45 24.45 38.32 5.36
360 380 2.826287 CACCACACGTTGCCCACA 60.826 61.111 0.00 0.00 0.00 4.17
361 381 2.044848 ACCACACGTTGCCCACAA 60.045 55.556 0.00 0.00 0.00 3.33
373 393 4.671549 CCACAACGCGCACTGCAG 62.672 66.667 13.48 13.48 46.97 4.41
384 404 1.665916 CACTGCAGTCCTCACCACG 60.666 63.158 18.64 0.00 0.00 4.94
392 412 2.108976 CCTCACCACGCACACACT 59.891 61.111 0.00 0.00 0.00 3.55
393 413 2.246739 CCTCACCACGCACACACTG 61.247 63.158 0.00 0.00 0.00 3.66
416 436 1.900981 CCGGAACATGCCCAACACA 60.901 57.895 0.00 0.00 0.00 3.72
421 441 1.001378 GAACATGCCCAACACAGTGAC 60.001 52.381 7.81 0.00 0.00 3.67
423 443 0.311790 CATGCCCAACACAGTGACAC 59.688 55.000 7.81 0.00 0.00 3.67
424 444 0.823356 ATGCCCAACACAGTGACACC 60.823 55.000 7.81 0.00 0.00 4.16
427 447 0.469917 CCCAACACAGTGACACCTCT 59.530 55.000 7.81 0.00 0.00 3.69
456 476 2.831685 TCTTTTGGCGAAGTGCTAGA 57.168 45.000 0.00 0.00 45.43 2.43
468 488 2.105930 GCTAGAGCACTGCCTCGG 59.894 66.667 0.00 0.00 41.59 4.63
469 489 2.716017 GCTAGAGCACTGCCTCGGT 61.716 63.158 0.00 0.00 41.59 4.69
476 496 1.959085 CACTGCCTCGGTGCATTTT 59.041 52.632 0.00 0.00 41.16 1.82
480 500 1.270550 CTGCCTCGGTGCATTTTCTTT 59.729 47.619 0.00 0.00 41.16 2.52
483 503 2.094545 GCCTCGGTGCATTTTCTTTCAT 60.095 45.455 0.00 0.00 0.00 2.57
486 506 4.159377 TCGGTGCATTTTCTTTCATGAC 57.841 40.909 0.00 0.00 0.00 3.06
491 511 5.451908 GTGCATTTTCTTTCATGACGAGAA 58.548 37.500 13.92 13.92 0.00 2.87
496 516 7.410087 GCATTTTCTTTCATGACGAGAAACATG 60.410 37.037 23.30 24.44 43.31 3.21
501 521 3.588955 TCATGACGAGAAACATGACTGG 58.411 45.455 0.00 0.00 44.86 4.00
523 543 5.355630 TGGAAGTCAAAGACGACATGAAAAA 59.644 36.000 0.00 0.00 38.43 1.94
542 562 7.992008 TGAAAAACTAGTTTGAACCACCTAAG 58.008 34.615 21.22 0.00 32.36 2.18
543 563 6.954487 AAAACTAGTTTGAACCACCTAAGG 57.046 37.500 21.22 0.00 32.36 2.69
546 566 6.449830 ACTAGTTTGAACCACCTAAGGAAT 57.550 37.500 0.00 0.00 0.00 3.01
547 567 6.473758 ACTAGTTTGAACCACCTAAGGAATC 58.526 40.000 0.00 0.00 0.00 2.52
549 569 5.701224 AGTTTGAACCACCTAAGGAATCAA 58.299 37.500 0.00 0.00 36.76 2.57
550 570 6.133356 AGTTTGAACCACCTAAGGAATCAAA 58.867 36.000 11.63 11.63 41.26 2.69
551 571 6.782494 AGTTTGAACCACCTAAGGAATCAAAT 59.218 34.615 15.80 7.71 43.11 2.32
553 573 8.749354 GTTTGAACCACCTAAGGAATCAAATAT 58.251 33.333 15.80 0.00 43.11 1.28
554 574 9.983024 TTTGAACCACCTAAGGAATCAAATATA 57.017 29.630 11.63 0.00 40.04 0.86
615 635 9.212641 TCATTCAATATTGCTATCTCTGCTAAC 57.787 33.333 10.76 0.00 0.00 2.34
641 661 7.792508 CGTAGCTAAAAATCATGAATCCGTAAC 59.207 37.037 0.00 0.00 0.00 2.50
654 674 4.823790 ATCCGTAACACCAACTTTGTTC 57.176 40.909 0.00 0.00 38.21 3.18
761 783 8.922931 TGAATTGAGTTATGTATATGGCATGT 57.077 30.769 10.98 6.03 0.00 3.21
856 6810 3.888930 CCAGCAGTTCAGGAGGTTTTTAA 59.111 43.478 0.00 0.00 0.00 1.52
948 6913 4.875561 AGGACTACAGAAGAGGAAACAC 57.124 45.455 0.00 0.00 0.00 3.32
959 6924 5.469084 AGAAGAGGAAACACAAACGTATTCC 59.531 40.000 0.00 0.00 39.85 3.01
1062 7048 0.249398 AGCATCTCCCCACGTTGTAC 59.751 55.000 0.00 0.00 0.00 2.90
1120 7114 1.298602 CAACGATGATGATGGCGGAA 58.701 50.000 0.00 0.00 0.00 4.30
1122 7116 1.299541 ACGATGATGATGGCGGAAAC 58.700 50.000 0.00 0.00 0.00 2.78
1127 7121 0.740737 GATGATGGCGGAAACCAAGG 59.259 55.000 0.00 0.00 44.65 3.61
1128 7122 0.684153 ATGATGGCGGAAACCAAGGG 60.684 55.000 0.00 0.00 44.65 3.95
1129 7123 2.679996 ATGGCGGAAACCAAGGGC 60.680 61.111 0.00 0.00 44.65 5.19
1133 7127 2.573340 CGGAAACCAAGGGCATGC 59.427 61.111 9.90 9.90 0.00 4.06
1306 7309 2.872842 GCCCGTTAAGCTGTTGTTCCTA 60.873 50.000 0.00 0.00 0.00 2.94
1330 7333 1.159098 GGACCGCGAGATACGACTCT 61.159 60.000 8.23 0.00 45.77 3.24
1384 7387 1.953138 GCGGCTGATCATCCTCACG 60.953 63.158 13.52 1.76 0.00 4.35
1456 7459 2.575993 CTCCTGCACGACCCTGAG 59.424 66.667 0.00 0.00 0.00 3.35
1477 7480 0.175073 GCGGGTTCTACGTCCTGAAT 59.825 55.000 4.08 0.00 32.26 2.57
1616 7621 2.737376 GCGACGGTGAGACAACCC 60.737 66.667 0.00 0.00 36.84 4.11
1629 7634 2.164338 GACAACCCGGGAAGCATTTAA 58.836 47.619 32.02 0.00 0.00 1.52
1678 7683 4.292178 GGAGATCGCTGGAGGCCG 62.292 72.222 0.00 0.00 37.74 6.13
1690 7695 1.357334 GAGGCCGATCTCTGTCGAC 59.643 63.158 9.11 9.11 44.06 4.20
1794 7803 0.679002 CACTGGCTCATCCACCCAAG 60.679 60.000 0.00 0.00 40.72 3.61
1795 7804 0.842030 ACTGGCTCATCCACCCAAGA 60.842 55.000 0.00 0.00 40.72 3.02
1799 7808 2.225343 TGGCTCATCCACCCAAGATTTT 60.225 45.455 0.00 0.00 40.72 1.82
1801 7810 4.218312 GGCTCATCCACCCAAGATTTTAT 58.782 43.478 0.00 0.00 34.01 1.40
2018 8035 0.391130 TAATGGTGACTGGTCGCTGC 60.391 55.000 12.94 0.00 39.85 5.25
2052 8069 4.117685 GACTTGGTACGGCTTGGTTATAG 58.882 47.826 0.00 0.00 0.00 1.31
2183 8200 7.400339 TCATGTCTCAAACCCTAGAACTAATCT 59.600 37.037 0.00 0.00 42.48 2.40
2186 8203 7.878127 TGTCTCAAACCCTAGAACTAATCTTTG 59.122 37.037 0.00 0.00 39.71 2.77
2211 8228 5.109903 ACTCGAAGGAATTTCTCGTTATGG 58.890 41.667 7.62 0.40 32.30 2.74
2283 8300 3.479370 GCAGAGGCACGTGTGATC 58.521 61.111 18.38 12.48 40.72 2.92
2284 8301 1.374631 GCAGAGGCACGTGTGATCA 60.375 57.895 18.38 0.00 40.72 2.92
2285 8302 0.950555 GCAGAGGCACGTGTGATCAA 60.951 55.000 18.38 0.00 40.72 2.57
2311 8328 3.024423 CAATGAATGCTGCACGGTG 57.976 52.632 3.57 3.15 0.00 4.94
2313 8330 0.523072 AATGAATGCTGCACGGTGTC 59.477 50.000 3.57 2.94 0.00 3.67
2317 8334 0.819259 AATGCTGCACGGTGTCAACT 60.819 50.000 3.57 0.00 0.00 3.16
2318 8335 1.230635 ATGCTGCACGGTGTCAACTC 61.231 55.000 3.57 2.26 0.00 3.01
2320 8337 0.319555 GCTGCACGGTGTCAACTCTA 60.320 55.000 10.24 0.00 0.00 2.43
2321 8338 1.419374 CTGCACGGTGTCAACTCTAC 58.581 55.000 10.24 0.00 0.00 2.59
2322 8339 0.318360 TGCACGGTGTCAACTCTACG 60.318 55.000 10.24 0.00 0.00 3.51
2479 8524 7.550196 AGGATTGGATCATGTTTAATTTGTTGC 59.450 33.333 0.00 0.00 0.00 4.17
2483 8528 5.861251 GGATCATGTTTAATTTGTTGCACGA 59.139 36.000 0.00 0.00 0.00 4.35
2493 8538 1.368641 TGTTGCACGATGTCATAGCC 58.631 50.000 0.00 0.00 0.00 3.93
2537 8582 9.424319 CTAATATTCTTGTTGTGTCACTACTGT 57.576 33.333 16.72 3.61 0.00 3.55
2558 8603 6.014840 ACTGTAATTTCTGAGTTTCCCGAGTA 60.015 38.462 0.00 0.00 0.00 2.59
2560 8605 5.485209 AATTTCTGAGTTTCCCGAGTACT 57.515 39.130 0.00 0.00 0.00 2.73
2614 8659 0.932399 AACGTGTTTGCCGAGTGTAC 59.068 50.000 0.00 0.00 0.00 2.90
2626 8679 3.021695 CCGAGTGTACTTCTGGTATCCA 58.978 50.000 0.00 0.00 32.56 3.41
2648 8701 1.256812 CCGAACCCTTCAGGCAAAAT 58.743 50.000 0.00 0.00 40.58 1.82
2657 8710 3.555586 CCTTCAGGCAAAATCCACTTTGG 60.556 47.826 0.00 0.00 36.89 3.28
2663 8716 2.627699 GCAAAATCCACTTTGGTGAGGA 59.372 45.455 0.00 0.00 45.61 3.71
2718 8771 8.299570 CAGTTGTAATTTGAAGCCTAGATTTGT 58.700 33.333 0.00 0.00 0.00 2.83
2742 8795 4.858692 CAGCTCCACCAAATTTACAATTCG 59.141 41.667 0.00 0.00 0.00 3.34
2759 8830 3.744238 TTCGGAGTGAACTGTCATCAA 57.256 42.857 0.00 0.00 35.80 2.57
2762 8833 4.245660 TCGGAGTGAACTGTCATCAATTC 58.754 43.478 0.00 0.00 35.80 2.17
2764 8835 4.326826 GGAGTGAACTGTCATCAATTCCA 58.673 43.478 8.37 0.00 35.80 3.53
2765 8836 4.394300 GGAGTGAACTGTCATCAATTCCAG 59.606 45.833 8.37 0.00 35.80 3.86
2769 8851 5.882557 GTGAACTGTCATCAATTCCAGGTAT 59.117 40.000 0.00 0.00 35.80 2.73
2883 8968 6.219473 CGCTTCATTCTTCCTAGATGTACAT 58.781 40.000 8.43 8.43 0.00 2.29
2900 8985 1.542915 ACATTGCCTGCAGATTGTCAC 59.457 47.619 17.39 0.00 0.00 3.67
2905 8990 2.089980 GCCTGCAGATTGTCACATTCT 58.910 47.619 17.39 0.00 0.00 2.40
2908 8993 3.622163 CCTGCAGATTGTCACATTCTCTC 59.378 47.826 17.39 0.00 0.00 3.20
2920 9005 6.071672 TGTCACATTCTCTCTAAGAGGAACTG 60.072 42.308 4.95 9.26 42.54 3.16
2933 9018 5.367945 AGAGGAACTGTAAAGTGTTTGGA 57.632 39.130 0.00 0.00 41.55 3.53
3002 9087 4.425180 TTATATAGCCAGCCGGAAACAA 57.575 40.909 5.05 0.00 0.00 2.83
3026 9111 1.770294 AAAAGGAACAGGGCGACAAA 58.230 45.000 0.00 0.00 0.00 2.83
3032 9117 2.231235 GGAACAGGGCGACAAATGAAAT 59.769 45.455 0.00 0.00 0.00 2.17
3039 9124 2.402305 GCGACAAATGAAATGGTGCAA 58.598 42.857 0.00 0.00 0.00 4.08
3048 9133 9.723601 ACAAATGAAATGGTGCAATAAAAGTAT 57.276 25.926 0.00 0.00 0.00 2.12
3081 9167 1.374631 AACAAGAGCATCGCGAGCA 60.375 52.632 25.12 0.88 42.67 4.26
3087 9173 3.121030 GCATCGCGAGCAGTTGGT 61.121 61.111 16.66 0.00 0.00 3.67
3192 9299 0.322546 GGTCCACCGCCTTTGAGATT 60.323 55.000 0.00 0.00 0.00 2.40
3337 9448 8.062065 TGTGTCATATGTGCTCGGATATAATA 57.938 34.615 1.90 0.00 0.00 0.98
3344 9455 6.710597 TGTGCTCGGATATAATATACTCCC 57.289 41.667 0.00 0.00 0.00 4.30
3345 9456 6.432581 TGTGCTCGGATATAATATACTCCCT 58.567 40.000 0.00 0.00 0.00 4.20
3346 9457 6.546403 TGTGCTCGGATATAATATACTCCCTC 59.454 42.308 0.00 0.00 0.00 4.30
3347 9458 6.773685 GTGCTCGGATATAATATACTCCCTCT 59.226 42.308 0.00 0.00 0.00 3.69
3348 9459 6.773200 TGCTCGGATATAATATACTCCCTCTG 59.227 42.308 0.00 0.00 0.00 3.35
3349 9460 6.773685 GCTCGGATATAATATACTCCCTCTGT 59.226 42.308 0.00 0.00 0.00 3.41
3351 9462 8.749026 TCGGATATAATATACTCCCTCTGTTC 57.251 38.462 0.00 0.00 0.00 3.18
3352 9463 8.558312 TCGGATATAATATACTCCCTCTGTTCT 58.442 37.037 0.00 0.00 0.00 3.01
3353 9464 8.625651 CGGATATAATATACTCCCTCTGTTCTG 58.374 40.741 0.00 0.00 0.00 3.02
3360 9471 9.440761 AATATACTCCCTCTGTTCTGAATTACT 57.559 33.333 0.00 0.00 0.00 2.24
3361 9472 7.741554 ATACTCCCTCTGTTCTGAATTACTT 57.258 36.000 0.00 0.00 0.00 2.24
3363 9474 5.308237 ACTCCCTCTGTTCTGAATTACTTGT 59.692 40.000 0.00 0.00 0.00 3.16
3364 9475 5.794894 TCCCTCTGTTCTGAATTACTTGTC 58.205 41.667 0.00 0.00 0.00 3.18
3366 9477 4.092091 CCTCTGTTCTGAATTACTTGTCGC 59.908 45.833 0.00 0.00 0.00 5.19
3367 9478 4.627058 TCTGTTCTGAATTACTTGTCGCA 58.373 39.130 0.00 0.00 0.00 5.10
3368 9479 5.237815 TCTGTTCTGAATTACTTGTCGCAT 58.762 37.500 0.00 0.00 0.00 4.73
3369 9480 5.120674 TCTGTTCTGAATTACTTGTCGCATG 59.879 40.000 0.00 0.00 0.00 4.06
3371 9482 5.929415 TGTTCTGAATTACTTGTCGCATGTA 59.071 36.000 0.00 2.87 0.00 2.29
3372 9483 6.593770 TGTTCTGAATTACTTGTCGCATGTAT 59.406 34.615 0.00 0.00 0.00 2.29
3373 9484 6.588348 TCTGAATTACTTGTCGCATGTATG 57.412 37.500 0.00 0.00 0.00 2.39
3374 9485 5.523552 TCTGAATTACTTGTCGCATGTATGG 59.476 40.000 0.00 0.00 0.00 2.74
3375 9486 5.423886 TGAATTACTTGTCGCATGTATGGA 58.576 37.500 0.00 0.00 0.00 3.41
3377 9488 5.929697 ATTACTTGTCGCATGTATGGATG 57.070 39.130 0.00 0.00 0.00 3.51
3380 9491 4.960938 ACTTGTCGCATGTATGGATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
3383 9494 5.975693 TGTCGCATGTATGGATGTATCTA 57.024 39.130 0.00 0.00 0.00 1.98
3384 9495 5.954335 TGTCGCATGTATGGATGTATCTAG 58.046 41.667 0.00 0.00 0.00 2.43
3385 9496 5.710099 TGTCGCATGTATGGATGTATCTAGA 59.290 40.000 0.00 0.00 0.00 2.43
3386 9497 6.378280 TGTCGCATGTATGGATGTATCTAGAT 59.622 38.462 10.73 10.73 0.00 1.98
3387 9498 6.694844 GTCGCATGTATGGATGTATCTAGATG 59.305 42.308 15.79 0.00 0.00 2.90
3388 9499 6.378280 TCGCATGTATGGATGTATCTAGATGT 59.622 38.462 15.79 1.25 0.00 3.06
3389 9500 7.556275 TCGCATGTATGGATGTATCTAGATGTA 59.444 37.037 15.79 4.44 0.00 2.29
3390 9501 8.355913 CGCATGTATGGATGTATCTAGATGTAT 58.644 37.037 15.79 9.11 0.00 2.29
3417 9528 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3418 9529 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3419 9530 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3420 9531 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3421 9532 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3422 9533 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3423 9534 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3424 9535 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3425 9536 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3426 9537 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3427 9538 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3428 9539 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
3429 9540 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
3430 9541 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
3431 9542 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
3432 9543 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
3433 9544 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
3434 9545 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
3928 10039 9.295214 CCTAACTAGCATATTTCATGATAGTCG 57.705 37.037 13.70 9.15 46.58 4.18
3939 10050 1.358877 TGATAGTCGCACATGCACAC 58.641 50.000 4.49 0.00 42.21 3.82
3940 10051 1.337635 TGATAGTCGCACATGCACACA 60.338 47.619 4.49 2.18 42.21 3.72
3941 10052 1.325640 GATAGTCGCACATGCACACAG 59.674 52.381 4.49 0.00 42.21 3.66
3942 10053 0.670239 TAGTCGCACATGCACACAGG 60.670 55.000 4.49 0.00 42.21 4.00
3943 10054 2.669229 TCGCACATGCACACAGGG 60.669 61.111 4.49 0.00 42.21 4.45
3944 10055 4.409218 CGCACATGCACACAGGGC 62.409 66.667 4.49 0.00 42.21 5.19
3945 10056 4.060038 GCACATGCACACAGGGCC 62.060 66.667 0.00 0.00 41.59 5.80
3946 10057 3.740397 CACATGCACACAGGGCCG 61.740 66.667 0.00 0.00 0.00 6.13
3949 10060 4.722700 ATGCACACAGGGCCGGTC 62.723 66.667 6.27 0.00 0.00 4.79
3952 10063 3.953775 CACACAGGGCCGGTCCTT 61.954 66.667 29.41 14.85 34.31 3.36
3953 10064 3.175710 ACACAGGGCCGGTCCTTT 61.176 61.111 29.41 18.93 34.31 3.11
3954 10065 2.359975 CACAGGGCCGGTCCTTTC 60.360 66.667 29.41 0.00 34.31 2.62
3955 10066 4.016706 ACAGGGCCGGTCCTTTCG 62.017 66.667 29.41 18.12 34.31 3.46
3956 10067 3.702048 CAGGGCCGGTCCTTTCGA 61.702 66.667 29.41 0.00 34.31 3.71
3957 10068 3.391382 AGGGCCGGTCCTTTCGAG 61.391 66.667 25.80 0.00 32.13 4.04
3958 10069 4.468689 GGGCCGGTCCTTTCGAGG 62.469 72.222 20.78 0.00 34.39 4.63
3959 10070 4.468689 GGCCGGTCCTTTCGAGGG 62.469 72.222 1.90 0.70 0.00 4.30
3960 10071 4.468689 GCCGGTCCTTTCGAGGGG 62.469 72.222 1.90 3.47 0.00 4.79
3961 10072 4.468689 CCGGTCCTTTCGAGGGGC 62.469 72.222 0.00 4.87 0.00 5.80
3962 10073 3.702048 CGGTCCTTTCGAGGGGCA 61.702 66.667 12.07 0.00 0.00 5.36
3963 10074 2.269241 GGTCCTTTCGAGGGGCAG 59.731 66.667 12.07 0.00 0.00 4.85
3964 10075 2.269241 GTCCTTTCGAGGGGCAGG 59.731 66.667 6.29 0.00 0.00 4.85
3965 10076 3.009115 TCCTTTCGAGGGGCAGGG 61.009 66.667 6.66 0.00 0.00 4.45
3966 10077 4.115199 CCTTTCGAGGGGCAGGGG 62.115 72.222 0.00 0.00 0.00 4.79
3967 10078 4.115199 CTTTCGAGGGGCAGGGGG 62.115 72.222 0.00 0.00 0.00 5.40
4004 10115 3.732849 CAAGACCAGGGCCCCCTC 61.733 72.222 21.43 10.78 46.28 4.30
4007 10118 4.103928 GACCAGGGCCCCCTCCTA 62.104 72.222 21.43 0.00 46.28 2.94
4008 10119 4.109656 ACCAGGGCCCCCTCCTAG 62.110 72.222 21.43 1.53 46.28 3.02
4009 10120 4.908274 CCAGGGCCCCCTCCTAGG 62.908 77.778 21.43 0.82 46.28 3.02
4010 10121 4.109656 CAGGGCCCCCTCCTAGGT 62.110 72.222 21.43 0.00 46.28 3.08
4011 10122 3.301811 AGGGCCCCCTCCTAGGTT 61.302 66.667 21.43 0.00 44.43 3.50
4012 10123 2.773053 GGGCCCCCTCCTAGGTTC 60.773 72.222 12.23 0.00 31.93 3.62
4013 10124 3.162154 GGCCCCCTCCTAGGTTCG 61.162 72.222 9.08 0.00 31.93 3.95
4014 10125 3.862991 GCCCCCTCCTAGGTTCGC 61.863 72.222 9.08 1.13 31.93 4.70
4015 10126 2.041819 CCCCCTCCTAGGTTCGCT 60.042 66.667 9.08 0.00 31.93 4.93
4016 10127 2.435693 CCCCCTCCTAGGTTCGCTG 61.436 68.421 9.08 0.00 31.93 5.18
4017 10128 2.435693 CCCCTCCTAGGTTCGCTGG 61.436 68.421 9.08 3.10 31.93 4.85
4018 10129 1.686110 CCCTCCTAGGTTCGCTGGT 60.686 63.158 9.08 0.00 31.93 4.00
4019 10130 0.396695 CCCTCCTAGGTTCGCTGGTA 60.397 60.000 9.08 0.00 31.93 3.25
4020 10131 1.033574 CCTCCTAGGTTCGCTGGTAG 58.966 60.000 9.08 0.00 0.00 3.18
4021 10132 0.386113 CTCCTAGGTTCGCTGGTAGC 59.614 60.000 9.08 0.00 38.02 3.58
4022 10133 1.041447 TCCTAGGTTCGCTGGTAGCC 61.041 60.000 9.08 0.00 38.18 3.93
4023 10134 1.442148 CTAGGTTCGCTGGTAGCCC 59.558 63.158 0.00 0.00 38.18 5.19
4024 10135 1.305465 TAGGTTCGCTGGTAGCCCA 60.305 57.895 0.00 0.00 38.18 5.36
4025 10136 0.689745 TAGGTTCGCTGGTAGCCCAT 60.690 55.000 0.00 0.00 40.90 4.00
4026 10137 1.819632 GGTTCGCTGGTAGCCCATG 60.820 63.158 0.00 0.00 40.90 3.66
4027 10138 1.819632 GTTCGCTGGTAGCCCATGG 60.820 63.158 4.14 4.14 40.90 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.322442 GAGCAATTATGAGCCACCCC 58.678 55.000 0.00 0.00 0.00 4.95
1 2 0.947244 CGAGCAATTATGAGCCACCC 59.053 55.000 0.00 0.00 0.00 4.61
2 3 0.947244 CCGAGCAATTATGAGCCACC 59.053 55.000 0.00 0.00 0.00 4.61
3 4 0.947244 CCCGAGCAATTATGAGCCAC 59.053 55.000 0.00 0.00 0.00 5.01
5 6 0.947244 CACCCGAGCAATTATGAGCC 59.053 55.000 0.00 0.00 0.00 4.70
6 7 0.308993 GCACCCGAGCAATTATGAGC 59.691 55.000 0.00 0.00 0.00 4.26
7 8 1.959042 AGCACCCGAGCAATTATGAG 58.041 50.000 0.00 0.00 36.85 2.90
12 13 1.959085 CACAAGCACCCGAGCAATT 59.041 52.632 0.00 0.00 36.85 2.32
13 14 2.629656 GCACAAGCACCCGAGCAAT 61.630 57.895 0.00 0.00 41.58 3.56
14 15 3.286751 GCACAAGCACCCGAGCAA 61.287 61.111 0.00 0.00 41.58 3.91
17 18 1.091771 CATAGGCACAAGCACCCGAG 61.092 60.000 0.00 0.00 44.61 4.63
18 19 1.078497 CATAGGCACAAGCACCCGA 60.078 57.895 0.00 0.00 44.61 5.14
19 20 2.764314 GCATAGGCACAAGCACCCG 61.764 63.158 0.00 0.00 44.61 5.28
20 21 3.200522 GCATAGGCACAAGCACCC 58.799 61.111 0.00 0.00 44.61 4.61
30 31 7.761249 AGACAAATTAAGACAAATTGCATAGGC 59.239 33.333 0.00 0.00 41.68 3.93
31 32 9.643693 AAGACAAATTAAGACAAATTGCATAGG 57.356 29.630 0.00 0.00 0.00 2.57
59 60 9.562583 CCAGATTCGTAGAAGCTAAGAATATAC 57.437 37.037 13.09 4.75 45.90 1.47
60 61 9.516546 TCCAGATTCGTAGAAGCTAAGAATATA 57.483 33.333 13.09 0.00 45.90 0.86
61 62 8.410673 TCCAGATTCGTAGAAGCTAAGAATAT 57.589 34.615 13.09 9.08 45.90 1.28
62 63 7.818997 TCCAGATTCGTAGAAGCTAAGAATA 57.181 36.000 13.09 0.00 45.90 1.75
63 64 6.716934 TCCAGATTCGTAGAAGCTAAGAAT 57.283 37.500 13.01 13.01 45.90 2.40
64 65 6.096987 ACATCCAGATTCGTAGAAGCTAAGAA 59.903 38.462 0.02 5.54 45.90 2.52
65 66 5.594725 ACATCCAGATTCGTAGAAGCTAAGA 59.405 40.000 0.02 2.10 45.90 2.10
66 67 5.837437 ACATCCAGATTCGTAGAAGCTAAG 58.163 41.667 0.02 0.00 45.90 2.18
67 68 5.854010 ACATCCAGATTCGTAGAAGCTAA 57.146 39.130 0.02 0.00 45.90 3.09
68 69 6.954487 TTACATCCAGATTCGTAGAAGCTA 57.046 37.500 0.02 0.00 45.90 3.32
69 70 5.854010 TTACATCCAGATTCGTAGAAGCT 57.146 39.130 0.00 0.00 45.90 3.74
70 71 7.484035 AAATTACATCCAGATTCGTAGAAGC 57.516 36.000 0.00 0.00 45.90 3.86
105 106 9.508642 TCAAACATTACAGTATAATGAACACCA 57.491 29.630 8.14 0.00 38.08 4.17
161 162 7.175641 CAGAGTGATCCTATTCACCAACTTTTT 59.824 37.037 1.19 0.00 45.80 1.94
162 163 6.656693 CAGAGTGATCCTATTCACCAACTTTT 59.343 38.462 1.19 0.00 45.80 2.27
163 164 6.176183 CAGAGTGATCCTATTCACCAACTTT 58.824 40.000 1.19 0.00 45.80 2.66
164 165 5.738909 CAGAGTGATCCTATTCACCAACTT 58.261 41.667 1.19 0.00 45.80 2.66
165 166 4.383552 GCAGAGTGATCCTATTCACCAACT 60.384 45.833 1.19 0.00 45.80 3.16
166 167 3.873952 GCAGAGTGATCCTATTCACCAAC 59.126 47.826 1.19 0.00 45.80 3.77
167 168 3.776969 AGCAGAGTGATCCTATTCACCAA 59.223 43.478 1.19 0.00 45.80 3.67
168 169 3.378512 AGCAGAGTGATCCTATTCACCA 58.621 45.455 1.19 0.00 45.80 4.17
169 170 3.386078 TGAGCAGAGTGATCCTATTCACC 59.614 47.826 1.19 0.00 45.80 4.02
170 171 4.142071 TGTGAGCAGAGTGATCCTATTCAC 60.142 45.833 0.00 0.00 45.15 3.18
171 172 4.026052 TGTGAGCAGAGTGATCCTATTCA 58.974 43.478 0.00 0.00 30.48 2.57
193 194 1.376037 GGCTCGTGCTTAGCAAGGT 60.376 57.895 18.93 0.00 41.47 3.50
196 197 1.671054 GGTGGCTCGTGCTTAGCAA 60.671 57.895 9.05 0.00 41.47 3.91
205 206 2.694829 GAACGTGTGAGGTGGCTCGT 62.695 60.000 0.00 0.00 36.58 4.18
206 207 2.022129 GAACGTGTGAGGTGGCTCG 61.022 63.158 0.00 0.00 0.00 5.03
212 213 1.752833 GGGGAAGAACGTGTGAGGT 59.247 57.895 0.00 0.00 0.00 3.85
217 218 2.280592 GTGCGGGGAAGAACGTGT 60.281 61.111 0.00 0.00 0.00 4.49
244 245 1.133407 CAAGTCTAGTGAGGAGGACGC 59.867 57.143 0.00 0.00 34.34 5.19
248 249 2.530701 ACCACAAGTCTAGTGAGGAGG 58.469 52.381 2.90 0.00 39.30 4.30
255 256 3.326588 TGCAATGGTACCACAAGTCTAGT 59.673 43.478 19.09 0.00 0.00 2.57
268 269 0.106894 TGTGTGACGGTGCAATGGTA 59.893 50.000 0.00 0.00 0.00 3.25
306 307 2.124151 CATTGGAAGGCGGGAGGG 60.124 66.667 0.00 0.00 0.00 4.30
308 309 1.750399 CCACATTGGAAGGCGGGAG 60.750 63.158 0.00 0.00 40.96 4.30
311 312 3.451894 GCCCACATTGGAAGGCGG 61.452 66.667 0.00 0.00 40.96 6.13
313 314 3.076916 GGGCCCACATTGGAAGGC 61.077 66.667 19.95 5.55 40.96 4.35
360 380 4.609018 AGGACTGCAGTGCGCGTT 62.609 61.111 29.46 12.13 46.97 4.84
365 385 1.963338 GTGGTGAGGACTGCAGTGC 60.963 63.158 29.04 29.04 36.57 4.40
372 392 2.421739 GTGTGCGTGGTGAGGACT 59.578 61.111 0.00 0.00 0.00 3.85
373 393 2.108157 TGTGTGCGTGGTGAGGAC 59.892 61.111 0.00 0.00 0.00 3.85
392 412 2.983030 GGCATGTTCCGGTGCACA 60.983 61.111 20.43 11.01 43.00 4.57
393 413 3.747976 GGGCATGTTCCGGTGCAC 61.748 66.667 15.76 8.80 43.00 4.57
416 436 3.567478 AGAAGCAAAAGAGGTGTCACT 57.433 42.857 2.35 0.00 0.00 3.41
421 441 5.045872 CCAAAAGAAGAAGCAAAAGAGGTG 58.954 41.667 0.00 0.00 0.00 4.00
423 443 4.053983 GCCAAAAGAAGAAGCAAAAGAGG 58.946 43.478 0.00 0.00 0.00 3.69
424 444 3.732721 CGCCAAAAGAAGAAGCAAAAGAG 59.267 43.478 0.00 0.00 0.00 2.85
427 447 3.791973 TCGCCAAAAGAAGAAGCAAAA 57.208 38.095 0.00 0.00 0.00 2.44
463 483 3.191162 TCATGAAAGAAAATGCACCGAGG 59.809 43.478 0.00 0.00 0.00 4.63
468 488 5.034554 TCTCGTCATGAAAGAAAATGCAC 57.965 39.130 0.00 0.00 0.00 4.57
469 489 5.687770 TTCTCGTCATGAAAGAAAATGCA 57.312 34.783 15.84 0.00 0.00 3.96
480 500 3.258123 TCCAGTCATGTTTCTCGTCATGA 59.742 43.478 0.00 0.00 45.07 3.07
483 503 3.069586 ACTTCCAGTCATGTTTCTCGTCA 59.930 43.478 0.00 0.00 0.00 4.35
496 516 3.093717 TGTCGTCTTTGACTTCCAGTC 57.906 47.619 0.00 0.00 45.26 3.51
501 521 6.487103 AGTTTTTCATGTCGTCTTTGACTTC 58.513 36.000 0.00 0.00 39.64 3.01
506 526 7.908082 TCAAACTAGTTTTTCATGTCGTCTTTG 59.092 33.333 18.25 2.57 0.00 2.77
507 527 7.981142 TCAAACTAGTTTTTCATGTCGTCTTT 58.019 30.769 18.25 0.00 0.00 2.52
523 543 5.899631 TTCCTTAGGTGGTTCAAACTAGT 57.100 39.130 0.00 0.00 0.00 2.57
586 606 9.955102 AGCAGAGATAGCAATATTGAATGATTA 57.045 29.630 19.73 2.00 0.00 1.75
587 607 8.865420 AGCAGAGATAGCAATATTGAATGATT 57.135 30.769 19.73 0.00 0.00 2.57
588 608 9.955102 TTAGCAGAGATAGCAATATTGAATGAT 57.045 29.630 19.73 5.69 0.00 2.45
589 609 9.212641 GTTAGCAGAGATAGCAATATTGAATGA 57.787 33.333 19.73 0.89 0.00 2.57
590 610 8.167345 CGTTAGCAGAGATAGCAATATTGAATG 58.833 37.037 19.73 7.01 0.00 2.67
591 611 7.875041 ACGTTAGCAGAGATAGCAATATTGAAT 59.125 33.333 19.73 11.06 0.00 2.57
592 612 7.210174 ACGTTAGCAGAGATAGCAATATTGAA 58.790 34.615 19.73 6.52 0.00 2.69
593 613 6.749139 ACGTTAGCAGAGATAGCAATATTGA 58.251 36.000 19.73 0.00 0.00 2.57
594 614 8.167523 CTACGTTAGCAGAGATAGCAATATTG 57.832 38.462 11.27 11.27 0.00 1.90
611 631 8.004344 CGGATTCATGATTTTTAGCTACGTTAG 58.996 37.037 0.00 0.00 0.00 2.34
615 635 6.287107 ACGGATTCATGATTTTTAGCTACG 57.713 37.500 0.00 0.00 0.00 3.51
754 776 4.637276 CCCGTGTTAGAATATACATGCCA 58.363 43.478 0.00 0.00 31.46 4.92
755 777 3.435671 GCCCGTGTTAGAATATACATGCC 59.564 47.826 0.00 0.00 31.46 4.40
757 779 4.637276 TGGCCCGTGTTAGAATATACATG 58.363 43.478 0.00 0.00 0.00 3.21
759 781 3.493699 GCTGGCCCGTGTTAGAATATACA 60.494 47.826 0.00 0.00 0.00 2.29
760 782 3.064931 GCTGGCCCGTGTTAGAATATAC 58.935 50.000 0.00 0.00 0.00 1.47
761 783 2.038033 GGCTGGCCCGTGTTAGAATATA 59.962 50.000 0.00 0.00 0.00 0.86
762 784 1.202770 GGCTGGCCCGTGTTAGAATAT 60.203 52.381 0.00 0.00 0.00 1.28
983 6948 7.830099 ACCAATTTCATCTCTGTCTTTCTTT 57.170 32.000 0.00 0.00 0.00 2.52
984 6949 7.830099 AACCAATTTCATCTCTGTCTTTCTT 57.170 32.000 0.00 0.00 0.00 2.52
985 6950 7.830099 AAACCAATTTCATCTCTGTCTTTCT 57.170 32.000 0.00 0.00 0.00 2.52
1120 7114 2.053865 CATCGGCATGCCCTTGGTT 61.054 57.895 30.79 9.04 0.00 3.67
1306 7309 1.653115 GTATCTCGCGGTCCGTGAT 59.347 57.895 26.79 20.65 45.17 3.06
1456 7459 1.139095 CAGGACGTAGAACCCGCTC 59.861 63.158 0.00 0.00 0.00 5.03
1552 7557 0.673644 CCTTGGTCTTGGCGTCGAAT 60.674 55.000 0.00 0.00 0.00 3.34
1608 7613 0.112412 AAATGCTTCCCGGGTTGTCT 59.888 50.000 22.86 0.50 0.00 3.41
1613 7618 1.615919 CCTGTTAAATGCTTCCCGGGT 60.616 52.381 22.86 0.50 0.00 5.28
1616 7621 0.455815 GCCCTGTTAAATGCTTCCCG 59.544 55.000 0.00 0.00 0.00 5.14
1678 7683 1.211818 GCATGCCGTCGACAGAGATC 61.212 60.000 17.16 0.00 0.00 2.75
2018 8035 2.743752 CCAAGTCCACGCGATGCTG 61.744 63.158 15.93 0.00 0.00 4.41
2052 8069 1.802960 CAGTCAGCACATGTCCTGTTC 59.197 52.381 16.32 10.78 35.29 3.18
2081 8098 3.181488 TGTTTGCCAACAACTCTGACATG 60.181 43.478 0.00 0.00 40.10 3.21
2183 8200 3.994392 CGAGAAATTCCTTCGAGTCCAAA 59.006 43.478 0.00 0.00 39.22 3.28
2186 8203 3.233684 ACGAGAAATTCCTTCGAGTCC 57.766 47.619 10.85 0.00 39.22 3.85
2211 8228 0.880278 TGCAACAGGTCGCTCAGTTC 60.880 55.000 0.00 0.00 0.00 3.01
2277 8294 5.708877 TTCATTGCTGTTGATTGATCACA 57.291 34.783 0.00 0.00 36.36 3.58
2278 8295 6.569228 CATTCATTGCTGTTGATTGATCAC 57.431 37.500 0.00 0.00 36.36 3.06
2311 8328 2.194271 GCATAGGCACGTAGAGTTGAC 58.806 52.381 0.00 0.00 40.72 3.18
2313 8330 1.137086 AGGCATAGGCACGTAGAGTTG 59.863 52.381 0.15 0.00 43.71 3.16
2317 8334 2.030551 CGAGGCATAGGCACGTAGA 58.969 57.895 0.15 0.00 43.71 2.59
2318 8335 1.661821 GCGAGGCATAGGCACGTAG 60.662 63.158 16.46 0.00 43.71 3.51
2320 8337 4.530857 GGCGAGGCATAGGCACGT 62.531 66.667 16.46 0.00 43.71 4.49
2459 8499 5.861251 TCGTGCAACAAATTAAACATGATCC 59.139 36.000 0.00 0.00 35.74 3.36
2483 8528 5.620206 TCATATTTTCCACGGCTATGACAT 58.380 37.500 0.00 0.00 0.00 3.06
2525 8570 7.948278 AACTCAGAAATTACAGTAGTGACAC 57.052 36.000 4.09 0.00 0.00 3.67
2537 8582 6.600882 AGTACTCGGGAAACTCAGAAATTA 57.399 37.500 0.00 0.00 0.00 1.40
2558 8603 4.224715 GCTTTTGCCGAGTTTTCTTAGT 57.775 40.909 0.00 0.00 40.15 2.24
2657 8710 1.604378 CCTGATGGGTGGTCCTCAC 59.396 63.158 0.00 0.00 45.34 3.51
2718 8771 5.335583 CGAATTGTAAATTTGGTGGAGCTGA 60.336 40.000 0.00 0.00 0.00 4.26
2742 8795 4.326826 TGGAATTGATGACAGTTCACTCC 58.673 43.478 0.00 1.67 42.09 3.85
2782 8864 7.855784 ACTTCTCCCAAAATAAGGTGAAAAT 57.144 32.000 0.00 0.00 35.76 1.82
2805 8887 8.962884 ATAATCCTTAAATGGCCATTCAAAAC 57.037 30.769 30.74 0.00 0.00 2.43
2848 8933 4.008074 AGAATGAAGCGGAAAGACTTGA 57.992 40.909 0.00 0.00 0.00 3.02
2883 8968 1.913778 ATGTGACAATCTGCAGGCAA 58.086 45.000 15.13 0.00 0.00 4.52
2900 8985 8.527810 ACTTTACAGTTCCTCTTAGAGAGAATG 58.472 37.037 11.32 10.16 45.07 2.67
2905 8990 7.598759 AACACTTTACAGTTCCTCTTAGAGA 57.401 36.000 11.32 0.00 0.00 3.10
2908 8993 6.990349 TCCAAACACTTTACAGTTCCTCTTAG 59.010 38.462 0.00 0.00 0.00 2.18
2920 9005 4.307443 AGCTTTGCTCCAAACACTTTAC 57.693 40.909 0.00 0.00 30.62 2.01
2933 9018 2.875094 ATTCCTGTGAGAGCTTTGCT 57.125 45.000 0.00 0.00 43.88 3.91
2994 9079 6.092748 CCTGTTCCTTTTATCATTGTTTCCG 58.907 40.000 0.00 0.00 0.00 4.30
3002 9087 3.279434 GTCGCCCTGTTCCTTTTATCAT 58.721 45.455 0.00 0.00 0.00 2.45
3053 9138 4.437794 GCGATGCTCTTGTTGAATGAATCA 60.438 41.667 0.00 0.00 35.85 2.57
3055 9140 3.486375 CGCGATGCTCTTGTTGAATGAAT 60.486 43.478 0.00 0.00 0.00 2.57
3081 9167 1.222115 GCGCACGAGAAGAACCAACT 61.222 55.000 0.30 0.00 0.00 3.16
3087 9173 1.660607 GATTGATGCGCACGAGAAGAA 59.339 47.619 14.90 0.00 0.00 2.52
3163 9270 1.227823 CGGTGGACCTGAGTTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
3192 9299 2.052782 TCGTCGATGAGGAGATGGAA 57.947 50.000 2.39 0.00 0.00 3.53
3308 9415 3.636764 TCCGAGCACATATGACACATACT 59.363 43.478 10.38 0.00 0.00 2.12
3337 9448 7.181125 ACAAGTAATTCAGAACAGAGGGAGTAT 59.819 37.037 0.00 0.00 0.00 2.12
3340 9451 5.799213 ACAAGTAATTCAGAACAGAGGGAG 58.201 41.667 0.00 0.00 0.00 4.30
3342 9453 4.627467 CGACAAGTAATTCAGAACAGAGGG 59.373 45.833 0.00 0.00 0.00 4.30
3344 9455 4.686091 TGCGACAAGTAATTCAGAACAGAG 59.314 41.667 0.00 0.00 0.00 3.35
3345 9456 4.627058 TGCGACAAGTAATTCAGAACAGA 58.373 39.130 0.00 0.00 0.00 3.41
3346 9457 4.990543 TGCGACAAGTAATTCAGAACAG 57.009 40.909 0.00 0.00 0.00 3.16
3347 9458 4.754618 ACATGCGACAAGTAATTCAGAACA 59.245 37.500 0.00 0.00 0.00 3.18
3348 9459 5.283060 ACATGCGACAAGTAATTCAGAAC 57.717 39.130 0.00 0.00 0.00 3.01
3349 9460 6.037062 CCATACATGCGACAAGTAATTCAGAA 59.963 38.462 0.00 0.00 0.00 3.02
3351 9462 5.523552 TCCATACATGCGACAAGTAATTCAG 59.476 40.000 0.00 0.00 0.00 3.02
3352 9463 5.423886 TCCATACATGCGACAAGTAATTCA 58.576 37.500 0.00 0.00 0.00 2.57
3353 9464 5.984233 TCCATACATGCGACAAGTAATTC 57.016 39.130 0.00 0.00 0.00 2.17
3355 9466 5.368145 ACATCCATACATGCGACAAGTAAT 58.632 37.500 0.00 0.00 0.00 1.89
3356 9467 4.765273 ACATCCATACATGCGACAAGTAA 58.235 39.130 0.00 0.00 0.00 2.24
3357 9468 4.400529 ACATCCATACATGCGACAAGTA 57.599 40.909 0.00 0.00 0.00 2.24
3358 9469 3.266510 ACATCCATACATGCGACAAGT 57.733 42.857 0.00 0.00 0.00 3.16
3359 9470 5.233225 AGATACATCCATACATGCGACAAG 58.767 41.667 0.00 0.00 0.00 3.16
3360 9471 5.213891 AGATACATCCATACATGCGACAA 57.786 39.130 0.00 0.00 0.00 3.18
3361 9472 4.871933 AGATACATCCATACATGCGACA 57.128 40.909 0.00 0.00 0.00 4.35
3363 9474 6.378280 ACATCTAGATACATCCATACATGCGA 59.622 38.462 4.54 0.00 0.00 5.10
3364 9475 6.567959 ACATCTAGATACATCCATACATGCG 58.432 40.000 4.54 0.00 0.00 4.73
3391 9502 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3392 9503 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3393 9504 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3394 9505 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3395 9506 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3396 9507 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3397 9508 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3398 9509 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3399 9510 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3400 9511 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3401 9512 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3402 9513 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3403 9514 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3404 9515 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3405 9516 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3406 9517 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3407 9518 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3408 9519 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
3409 9520 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3410 9521 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3411 9522 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3412 9523 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3413 9524 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3414 9525 3.369835 GTTCCAAATTACTCGTCGCAG 57.630 47.619 0.00 0.00 0.00 5.18
3928 10039 4.060038 GGCCCTGTGTGCATGTGC 62.060 66.667 0.00 0.00 42.50 4.57
3939 10050 3.665675 CTCGAAAGGACCGGCCCTG 62.666 68.421 11.33 0.00 36.49 4.45
3940 10051 3.391382 CTCGAAAGGACCGGCCCT 61.391 66.667 2.07 2.07 38.42 5.19
3941 10052 4.468689 CCTCGAAAGGACCGGCCC 62.469 72.222 0.00 0.00 46.67 5.80
3942 10053 4.468689 CCCTCGAAAGGACCGGCC 62.469 72.222 0.00 3.58 46.67 6.13
3943 10054 4.468689 CCCCTCGAAAGGACCGGC 62.469 72.222 0.00 0.00 46.67 6.13
3944 10055 4.468689 GCCCCTCGAAAGGACCGG 62.469 72.222 0.00 0.00 46.67 5.28
3945 10056 3.665675 CTGCCCCTCGAAAGGACCG 62.666 68.421 4.58 0.00 46.67 4.79
3946 10057 2.269241 CTGCCCCTCGAAAGGACC 59.731 66.667 4.58 0.00 46.67 4.46
3947 10058 2.269241 CCTGCCCCTCGAAAGGAC 59.731 66.667 4.58 0.00 46.67 3.85
3948 10059 3.009115 CCCTGCCCCTCGAAAGGA 61.009 66.667 4.58 0.00 46.67 3.36
3949 10060 4.115199 CCCCTGCCCCTCGAAAGG 62.115 72.222 0.00 0.00 42.95 3.11
3950 10061 4.115199 CCCCCTGCCCCTCGAAAG 62.115 72.222 0.00 0.00 0.00 2.62
3995 10106 2.773053 GAACCTAGGAGGGGGCCC 60.773 72.222 17.98 15.76 40.58 5.80
3996 10107 3.162154 CGAACCTAGGAGGGGGCC 61.162 72.222 17.98 0.00 40.58 5.80
3997 10108 3.862991 GCGAACCTAGGAGGGGGC 61.863 72.222 17.98 7.51 40.58 5.80
3998 10109 2.041819 AGCGAACCTAGGAGGGGG 60.042 66.667 17.98 0.68 40.58 5.40
3999 10110 2.435693 CCAGCGAACCTAGGAGGGG 61.436 68.421 17.98 4.08 40.58 4.79
4000 10111 0.396695 TACCAGCGAACCTAGGAGGG 60.397 60.000 17.98 9.41 40.58 4.30
4001 10112 1.033574 CTACCAGCGAACCTAGGAGG 58.966 60.000 17.98 9.40 42.49 4.30
4002 10113 0.386113 GCTACCAGCGAACCTAGGAG 59.614 60.000 17.98 7.54 0.00 3.69
4003 10114 1.041447 GGCTACCAGCGAACCTAGGA 61.041 60.000 17.98 0.00 43.62 2.94
4004 10115 1.442148 GGCTACCAGCGAACCTAGG 59.558 63.158 7.41 7.41 43.62 3.02
4005 10116 1.327690 TGGGCTACCAGCGAACCTAG 61.328 60.000 0.00 0.00 43.62 3.02
4006 10117 1.305465 TGGGCTACCAGCGAACCTA 60.305 57.895 0.00 0.00 43.62 3.08
4007 10118 2.606519 TGGGCTACCAGCGAACCT 60.607 61.111 0.00 0.00 43.62 3.50


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

AutoCloner maintained by Alex Coulton.