Multiple sequence alignment - TraesCS1D01G248200

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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 TraesCS1D01G248200 chr1D 100.000 2804 0 0 1 2804 341177793 341174990 0.000000e+00 5179.0
1 TraesCS1D01G248200 chr1D 96.000 50 2 0 478 527 47705729 47705778 6.440000e-12 82.4
2 TraesCS1D01G248200 chr1B 90.115 1659 87 25 1201 2804 456840133 456838497 0.000000e+00 2084.0
3 TraesCS1D01G248200 chr1B 85.579 527 40 19 651 1156 456840645 456840134 1.150000e-143 520.0
4 TraesCS1D01G248200 chr1B 93.548 93 5 1 528 619 15465048 15465140 1.350000e-28 137.0
5 TraesCS1D01G248200 chr1B 90.099 101 7 3 528 627 19056005 19056103 8.150000e-26 128.0
6 TraesCS1D01G248200 chr1A 85.439 1923 160 54 625 2497 440802329 440800477 0.000000e+00 1890.0
7 TraesCS1D01G248200 chr1A 87.345 403 21 9 104 483 440802728 440802333 4.290000e-118 435.0
8 TraesCS1D01G248200 chr1A 86.331 278 23 5 2542 2804 440800488 440800211 3.530000e-74 289.0
9 TraesCS1D01G248200 chr7D 89.552 134 11 3 482 613 113115994 113116126 1.730000e-37 167.0
10 TraesCS1D01G248200 chr7D 97.826 46 1 0 482 527 25386516 25386561 2.320000e-11 80.5
11 TraesCS1D01G248200 chr5B 96.552 87 2 1 528 613 459489914 459490000 2.910000e-30 143.0
12 TraesCS1D01G248200 chr5B 91.667 96 6 2 528 622 490726277 490726183 6.300000e-27 132.0
13 TraesCS1D01G248200 chr2B 96.552 87 2 1 528 613 799714023 799714109 2.910000e-30 143.0
14 TraesCS1D01G248200 chr2B 94.545 55 3 0 476 530 667132963 667133017 4.980000e-13 86.1
15 TraesCS1D01G248200 chr4B 95.506 89 3 1 528 615 392046839 392046927 1.050000e-29 141.0
16 TraesCS1D01G248200 chr4B 97.826 46 1 0 482 527 667579462 667579507 2.320000e-11 80.5
17 TraesCS1D01G248200 chr3B 95.455 88 3 1 528 614 750005451 750005364 3.770000e-29 139.0
18 TraesCS1D01G248200 chr7B 87.963 108 11 2 528 634 259789053 259788947 2.930000e-25 126.0
19 TraesCS1D01G248200 chr7B 92.453 53 3 1 475 527 523274587 523274638 1.080000e-09 75.0
20 TraesCS1D01G248200 chr6B 96.000 50 2 0 478 527 95348585 95348536 6.440000e-12 82.4
21 TraesCS1D01G248200 chr6B 90.000 60 4 2 469 527 545317941 545317883 3.000000e-10 76.8
22 TraesCS1D01G248200 chr4A 97.826 46 1 0 482 527 620326012 620326057 2.320000e-11 80.5
23 TraesCS1D01G248200 chr5A 97.619 42 1 0 244 285 469231767 469231726 3.870000e-09 73.1


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 TraesCS1D01G248200 chr1D 341174990 341177793 2803 True 5179.000000 5179 100.000000 1 2804 1 chr1D.!!$R1 2803
1 TraesCS1D01G248200 chr1B 456838497 456840645 2148 True 1302.000000 2084 87.847000 651 2804 2 chr1B.!!$R1 2153
2 TraesCS1D01G248200 chr1A 440800211 440802728 2517 True 871.333333 1890 86.371667 104 2804 3 chr1A.!!$R1 2700

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
617 640 0.100861 CGAACGGAGGGAGTAGAAGC 59.899 60.0 0.00 0.00 0.00 3.86 F
639 662 0.239347 AACTGCACAAGCGCTGAATC 59.761 50.0 12.58 1.31 46.23 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1812 0.397254 GGAGGACGAGGAGGATGGAA 60.397 60.0 0.0 0.0 0.0 3.53 R
2269 2363 0.546598 CCCCAATCTCTTACCCGCTT 59.453 55.0 0.0 0.0 0.0 4.68 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 2.775856 TTGCTCTAGGCGCTCTCGG 61.776 63.158 7.64 0.25 45.43 4.63
19 20 3.213402 GCTCTAGGCGCTCTCGGT 61.213 66.667 7.64 0.00 35.95 4.69
20 21 3.027292 CTCTAGGCGCTCTCGGTC 58.973 66.667 7.64 0.00 35.95 4.79
21 22 2.887889 CTCTAGGCGCTCTCGGTCG 61.888 68.421 7.64 0.00 35.95 4.79
22 23 2.895865 CTAGGCGCTCTCGGTCGA 60.896 66.667 7.64 0.00 35.95 4.20
23 24 2.887889 CTAGGCGCTCTCGGTCGAG 61.888 68.421 7.64 13.56 43.21 4.04
32 33 2.404923 TCTCGGTCGAGATGTTCTCT 57.595 50.000 17.73 0.00 45.26 3.10
33 34 2.712709 TCTCGGTCGAGATGTTCTCTT 58.287 47.619 17.73 0.00 45.26 2.85
34 35 3.082548 TCTCGGTCGAGATGTTCTCTTT 58.917 45.455 17.73 0.00 45.26 2.52
35 36 3.119814 TCTCGGTCGAGATGTTCTCTTTG 60.120 47.826 17.73 0.00 45.26 2.77
36 37 2.557056 TCGGTCGAGATGTTCTCTTTGT 59.443 45.455 3.27 0.00 41.26 2.83
37 38 2.663602 CGGTCGAGATGTTCTCTTTGTG 59.336 50.000 3.27 0.00 41.26 3.33
38 39 3.654414 GGTCGAGATGTTCTCTTTGTGT 58.346 45.455 3.27 0.00 41.26 3.72
39 40 3.675698 GGTCGAGATGTTCTCTTTGTGTC 59.324 47.826 3.27 0.00 41.26 3.67
40 41 4.551388 GTCGAGATGTTCTCTTTGTGTCT 58.449 43.478 3.27 0.00 41.26 3.41
41 42 4.985409 GTCGAGATGTTCTCTTTGTGTCTT 59.015 41.667 3.27 0.00 41.26 3.01
42 43 5.117897 GTCGAGATGTTCTCTTTGTGTCTTC 59.882 44.000 3.27 0.00 41.26 2.87
43 44 4.387256 CGAGATGTTCTCTTTGTGTCTTCC 59.613 45.833 3.27 0.00 41.26 3.46
44 45 4.310769 AGATGTTCTCTTTGTGTCTTCCG 58.689 43.478 0.00 0.00 0.00 4.30
45 46 2.210116 TGTTCTCTTTGTGTCTTCCGC 58.790 47.619 0.00 0.00 0.00 5.54
46 47 2.158957 TGTTCTCTTTGTGTCTTCCGCT 60.159 45.455 0.00 0.00 0.00 5.52
47 48 2.154854 TCTCTTTGTGTCTTCCGCTG 57.845 50.000 0.00 0.00 0.00 5.18
48 49 1.686587 TCTCTTTGTGTCTTCCGCTGA 59.313 47.619 0.00 0.00 0.00 4.26
49 50 2.300152 TCTCTTTGTGTCTTCCGCTGAT 59.700 45.455 0.00 0.00 0.00 2.90
50 51 2.670414 CTCTTTGTGTCTTCCGCTGATC 59.330 50.000 0.00 0.00 0.00 2.92
51 52 2.037121 TCTTTGTGTCTTCCGCTGATCA 59.963 45.455 0.00 0.00 0.00 2.92
52 53 2.542020 TTGTGTCTTCCGCTGATCAA 57.458 45.000 0.00 0.00 0.00 2.57
53 54 2.084610 TGTGTCTTCCGCTGATCAAG 57.915 50.000 0.00 0.00 0.00 3.02
54 55 1.344438 TGTGTCTTCCGCTGATCAAGT 59.656 47.619 0.00 0.00 0.00 3.16
55 56 2.224281 TGTGTCTTCCGCTGATCAAGTT 60.224 45.455 0.00 0.00 0.00 2.66
56 57 3.006430 TGTGTCTTCCGCTGATCAAGTTA 59.994 43.478 0.00 0.00 0.00 2.24
57 58 3.368236 GTGTCTTCCGCTGATCAAGTTAC 59.632 47.826 0.00 0.00 0.00 2.50
58 59 3.258372 TGTCTTCCGCTGATCAAGTTACT 59.742 43.478 0.00 0.00 0.00 2.24
59 60 4.461431 TGTCTTCCGCTGATCAAGTTACTA 59.539 41.667 0.00 0.00 0.00 1.82
60 61 5.047590 TGTCTTCCGCTGATCAAGTTACTAA 60.048 40.000 0.00 0.00 0.00 2.24
61 62 5.517054 GTCTTCCGCTGATCAAGTTACTAAG 59.483 44.000 0.00 0.00 0.00 2.18
62 63 4.386867 TCCGCTGATCAAGTTACTAAGG 57.613 45.455 0.00 0.00 0.00 2.69
63 64 4.021229 TCCGCTGATCAAGTTACTAAGGA 58.979 43.478 0.00 0.00 0.00 3.36
64 65 4.649674 TCCGCTGATCAAGTTACTAAGGAT 59.350 41.667 0.00 0.00 0.00 3.24
65 66 5.128827 TCCGCTGATCAAGTTACTAAGGATT 59.871 40.000 0.00 0.00 0.00 3.01
66 67 5.817816 CCGCTGATCAAGTTACTAAGGATTT 59.182 40.000 0.00 0.00 0.00 2.17
67 68 6.984474 CCGCTGATCAAGTTACTAAGGATTTA 59.016 38.462 0.00 0.00 0.00 1.40
68 69 7.042658 CCGCTGATCAAGTTACTAAGGATTTAC 60.043 40.741 0.00 0.00 0.00 2.01
69 70 7.707035 CGCTGATCAAGTTACTAAGGATTTACT 59.293 37.037 0.00 0.00 0.00 2.24
70 71 8.821894 GCTGATCAAGTTACTAAGGATTTACTG 58.178 37.037 0.00 0.00 0.00 2.74
71 72 9.877178 CTGATCAAGTTACTAAGGATTTACTGT 57.123 33.333 0.00 0.00 0.00 3.55
79 80 9.070149 GTTACTAAGGATTTACTGTACTGAACG 57.930 37.037 6.77 0.00 0.00 3.95
80 81 7.458409 ACTAAGGATTTACTGTACTGAACGA 57.542 36.000 6.77 0.00 0.00 3.85
81 82 7.536855 ACTAAGGATTTACTGTACTGAACGAG 58.463 38.462 6.77 0.00 0.00 4.18
82 83 4.745649 AGGATTTACTGTACTGAACGAGC 58.254 43.478 6.77 0.00 0.00 5.03
83 84 4.219944 AGGATTTACTGTACTGAACGAGCA 59.780 41.667 6.77 0.00 0.00 4.26
84 85 4.927425 GGATTTACTGTACTGAACGAGCAA 59.073 41.667 6.77 0.00 0.00 3.91
85 86 5.163982 GGATTTACTGTACTGAACGAGCAAC 60.164 44.000 6.77 0.00 0.00 4.17
86 87 4.579454 TTACTGTACTGAACGAGCAACT 57.421 40.909 6.77 0.00 0.00 3.16
87 88 5.694231 TTACTGTACTGAACGAGCAACTA 57.306 39.130 6.77 0.00 0.00 2.24
88 89 4.579454 ACTGTACTGAACGAGCAACTAA 57.421 40.909 6.77 0.00 0.00 2.24
89 90 4.547532 ACTGTACTGAACGAGCAACTAAG 58.452 43.478 6.77 0.00 0.00 2.18
90 91 3.909430 TGTACTGAACGAGCAACTAAGG 58.091 45.455 0.00 0.00 0.00 2.69
91 92 3.319972 TGTACTGAACGAGCAACTAAGGT 59.680 43.478 0.00 0.00 0.00 3.50
92 93 2.755650 ACTGAACGAGCAACTAAGGTG 58.244 47.619 0.00 0.00 0.00 4.00
93 94 2.364324 ACTGAACGAGCAACTAAGGTGA 59.636 45.455 0.00 0.00 0.00 4.02
94 95 3.006967 ACTGAACGAGCAACTAAGGTGAT 59.993 43.478 0.00 0.00 0.00 3.06
95 96 3.325870 TGAACGAGCAACTAAGGTGATG 58.674 45.455 0.00 0.00 0.00 3.07
96 97 1.726853 ACGAGCAACTAAGGTGATGC 58.273 50.000 0.00 0.00 39.06 3.91
100 101 2.350522 AGCAACTAAGGTGATGCTTCG 58.649 47.619 0.00 0.00 46.36 3.79
101 102 2.028112 AGCAACTAAGGTGATGCTTCGA 60.028 45.455 0.00 0.00 46.36 3.71
102 103 2.939103 GCAACTAAGGTGATGCTTCGAT 59.061 45.455 0.00 0.00 35.93 3.59
103 104 3.242543 GCAACTAAGGTGATGCTTCGATG 60.243 47.826 0.00 0.00 35.93 3.84
104 105 3.185246 ACTAAGGTGATGCTTCGATGG 57.815 47.619 0.00 0.00 0.00 3.51
105 106 2.766263 ACTAAGGTGATGCTTCGATGGA 59.234 45.455 0.00 0.00 0.00 3.41
106 107 3.389329 ACTAAGGTGATGCTTCGATGGAT 59.611 43.478 4.95 4.95 0.00 3.41
107 108 2.251409 AGGTGATGCTTCGATGGATG 57.749 50.000 10.06 0.00 0.00 3.51
108 109 1.764723 AGGTGATGCTTCGATGGATGA 59.235 47.619 10.06 0.00 0.00 2.92
109 110 2.371179 AGGTGATGCTTCGATGGATGAT 59.629 45.455 10.06 0.00 0.00 2.45
110 111 3.580022 AGGTGATGCTTCGATGGATGATA 59.420 43.478 10.06 0.00 0.00 2.15
111 112 3.681897 GGTGATGCTTCGATGGATGATAC 59.318 47.826 10.06 6.50 0.00 2.24
112 113 4.562347 GGTGATGCTTCGATGGATGATACT 60.562 45.833 10.06 0.00 0.00 2.12
113 114 4.388165 GTGATGCTTCGATGGATGATACTG 59.612 45.833 10.06 0.00 0.00 2.74
114 115 4.039609 TGATGCTTCGATGGATGATACTGT 59.960 41.667 10.06 0.00 0.00 3.55
115 116 5.243730 TGATGCTTCGATGGATGATACTGTA 59.756 40.000 10.06 0.00 0.00 2.74
116 117 5.728637 TGCTTCGATGGATGATACTGTAT 57.271 39.130 0.00 0.00 0.00 2.29
117 118 6.101650 TGCTTCGATGGATGATACTGTATT 57.898 37.500 1.22 0.00 0.00 1.89
118 119 5.928264 TGCTTCGATGGATGATACTGTATTG 59.072 40.000 1.22 0.00 0.00 1.90
119 120 5.163913 GCTTCGATGGATGATACTGTATTGC 60.164 44.000 1.22 0.00 0.00 3.56
120 121 4.820897 TCGATGGATGATACTGTATTGCC 58.179 43.478 1.22 4.98 0.00 4.52
151 152 3.483808 TTGTAGCATGACCAGTTGTGA 57.516 42.857 0.00 0.00 0.00 3.58
200 201 5.239963 TCGTAATCCTGTATACGATCAAGCA 59.760 40.000 4.12 0.00 46.24 3.91
224 234 9.314321 GCATCGCTGTATTAGTAATACCAATAT 57.686 33.333 23.98 13.23 42.41 1.28
229 239 7.011109 GCTGTATTAGTAATACCAATATGGCCG 59.989 40.741 23.98 6.61 42.67 6.13
234 244 2.806945 ATACCAATATGGCCGGATGG 57.193 50.000 5.05 13.39 42.67 3.51
243 253 2.348998 GCCGGATGGGATAGGCTG 59.651 66.667 5.05 0.00 45.67 4.85
287 304 4.617808 TCAGATAGAGCACGTTGACTAC 57.382 45.455 0.00 0.00 0.00 2.73
324 341 3.681594 GCAACCCCTAACGAGAATCATGA 60.682 47.826 0.00 0.00 33.17 3.07
332 349 5.863935 CCTAACGAGAATCATGAATGCGATA 59.136 40.000 14.64 8.29 33.17 2.92
337 354 4.453478 GAGAATCATGAATGCGATAGGCAA 59.547 41.667 0.00 0.00 46.48 4.52
351 368 0.250901 AGGCAAGTGAAAGCGATGGT 60.251 50.000 0.00 0.00 0.00 3.55
406 423 1.808945 CCATTGCTTGTCTGACTGACC 59.191 52.381 9.51 0.00 44.75 4.02
407 424 2.497138 CATTGCTTGTCTGACTGACCA 58.503 47.619 9.51 0.00 44.75 4.02
408 425 2.708216 TTGCTTGTCTGACTGACCAA 57.292 45.000 9.51 4.72 44.75 3.67
409 426 1.953559 TGCTTGTCTGACTGACCAAC 58.046 50.000 9.51 0.60 44.75 3.77
410 427 1.230324 GCTTGTCTGACTGACCAACC 58.770 55.000 9.51 0.00 44.75 3.77
411 428 1.502231 CTTGTCTGACTGACCAACCG 58.498 55.000 9.51 0.00 44.75 4.44
440 457 9.528489 ACTGGTGTACAACTTCCATTTTATTAT 57.472 29.630 13.07 0.00 0.00 1.28
444 461 9.567848 GTGTACAACTTCCATTTTATTATGGTG 57.432 33.333 0.00 0.00 44.48 4.17
454 477 7.285172 TCCATTTTATTATGGTGTGGATGTCAG 59.715 37.037 0.00 0.00 44.48 3.51
462 485 0.325933 TGTGGATGTCAGCTTCCCTG 59.674 55.000 0.00 0.00 43.17 4.45
466 489 2.244117 GATGTCAGCTTCCCTGCCGA 62.244 60.000 0.00 0.00 41.50 5.54
483 506 3.868661 TGCCGATATCACACACAATGTAC 59.131 43.478 3.12 0.00 40.64 2.90
484 507 4.119862 GCCGATATCACACACAATGTACT 58.880 43.478 3.12 0.00 40.64 2.73
485 508 4.209288 GCCGATATCACACACAATGTACTC 59.791 45.833 3.12 0.00 40.64 2.59
486 509 4.745125 CCGATATCACACACAATGTACTCC 59.255 45.833 3.12 0.00 40.64 3.85
487 510 4.745125 CGATATCACACACAATGTACTCCC 59.255 45.833 3.12 0.00 40.64 4.30
488 511 5.451937 CGATATCACACACAATGTACTCCCT 60.452 44.000 3.12 0.00 40.64 4.20
489 512 3.678056 TCACACACAATGTACTCCCTC 57.322 47.619 0.00 0.00 40.64 4.30
490 513 2.301870 TCACACACAATGTACTCCCTCC 59.698 50.000 0.00 0.00 40.64 4.30
491 514 1.275291 ACACACAATGTACTCCCTCCG 59.725 52.381 0.00 0.00 40.88 4.63
492 515 1.275291 CACACAATGTACTCCCTCCGT 59.725 52.381 0.00 0.00 0.00 4.69
493 516 1.975680 ACACAATGTACTCCCTCCGTT 59.024 47.619 0.00 0.00 0.00 4.44
494 517 2.370849 ACACAATGTACTCCCTCCGTTT 59.629 45.455 0.00 0.00 0.00 3.60
495 518 2.742053 CACAATGTACTCCCTCCGTTTG 59.258 50.000 0.00 0.00 0.00 2.93
496 519 2.290071 ACAATGTACTCCCTCCGTTTGG 60.290 50.000 0.00 0.00 0.00 3.28
497 520 1.946984 ATGTACTCCCTCCGTTTGGA 58.053 50.000 0.00 0.00 43.88 3.53
498 521 1.719529 TGTACTCCCTCCGTTTGGAA 58.280 50.000 0.00 0.00 45.87 3.53
499 522 2.262637 TGTACTCCCTCCGTTTGGAAT 58.737 47.619 0.00 0.00 45.87 3.01
500 523 2.640826 TGTACTCCCTCCGTTTGGAATT 59.359 45.455 0.00 0.00 45.87 2.17
501 524 3.839490 TGTACTCCCTCCGTTTGGAATTA 59.161 43.478 0.00 0.00 45.87 1.40
502 525 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
503 526 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
504 527 3.329814 ACTCCCTCCGTTTGGAATTACTT 59.670 43.478 0.00 0.00 45.87 2.24
505 528 3.681593 TCCCTCCGTTTGGAATTACTTG 58.318 45.455 0.00 0.00 45.87 3.16
506 529 3.073356 TCCCTCCGTTTGGAATTACTTGT 59.927 43.478 0.00 0.00 45.87 3.16
507 530 3.439129 CCCTCCGTTTGGAATTACTTGTC 59.561 47.826 0.00 0.00 45.87 3.18
508 531 4.069304 CCTCCGTTTGGAATTACTTGTCA 58.931 43.478 0.00 0.00 45.87 3.58
509 532 4.700213 CCTCCGTTTGGAATTACTTGTCAT 59.300 41.667 0.00 0.00 45.87 3.06
510 533 5.878116 CCTCCGTTTGGAATTACTTGTCATA 59.122 40.000 0.00 0.00 45.87 2.15
511 534 6.373216 CCTCCGTTTGGAATTACTTGTCATAA 59.627 38.462 0.00 0.00 45.87 1.90
512 535 7.094549 CCTCCGTTTGGAATTACTTGTCATAAA 60.095 37.037 0.00 0.00 45.87 1.40
513 536 8.167605 TCCGTTTGGAATTACTTGTCATAAAA 57.832 30.769 0.00 0.00 42.85 1.52
514 537 8.630917 TCCGTTTGGAATTACTTGTCATAAAAA 58.369 29.630 0.00 0.00 42.85 1.94
515 538 9.418045 CCGTTTGGAATTACTTGTCATAAAAAT 57.582 29.630 0.00 0.00 37.49 1.82
604 627 5.539582 TTTTGATGAGTAATTCCGAACGG 57.460 39.130 6.94 6.94 0.00 4.44
605 628 4.459390 TTGATGAGTAATTCCGAACGGA 57.541 40.909 12.04 12.04 43.52 4.69
606 629 4.041740 TGATGAGTAATTCCGAACGGAG 57.958 45.455 15.34 0.00 46.06 4.63
607 630 2.953466 TGAGTAATTCCGAACGGAGG 57.047 50.000 15.34 0.00 46.06 4.30
608 631 1.479323 TGAGTAATTCCGAACGGAGGG 59.521 52.381 15.34 0.00 46.06 4.30
609 632 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
610 633 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
611 634 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
612 635 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
613 636 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
614 637 0.329261 TTCCGAACGGAGGGAGTAGA 59.671 55.000 15.34 0.00 46.06 2.59
615 638 0.329261 TCCGAACGGAGGGAGTAGAA 59.671 55.000 12.04 0.00 39.76 2.10
616 639 0.739561 CCGAACGGAGGGAGTAGAAG 59.260 60.000 7.53 0.00 37.50 2.85
617 640 0.100861 CGAACGGAGGGAGTAGAAGC 59.899 60.000 0.00 0.00 0.00 3.86
618 641 1.183549 GAACGGAGGGAGTAGAAGCA 58.816 55.000 0.00 0.00 0.00 3.91
619 642 0.896226 AACGGAGGGAGTAGAAGCAC 59.104 55.000 0.00 0.00 0.00 4.40
620 643 0.251653 ACGGAGGGAGTAGAAGCACA 60.252 55.000 0.00 0.00 0.00 4.57
621 644 0.895530 CGGAGGGAGTAGAAGCACAA 59.104 55.000 0.00 0.00 0.00 3.33
622 645 1.404315 CGGAGGGAGTAGAAGCACAAC 60.404 57.143 0.00 0.00 0.00 3.32
623 646 1.903183 GGAGGGAGTAGAAGCACAACT 59.097 52.381 0.00 0.00 0.00 3.16
631 654 0.383231 AGAAGCACAACTGCACAAGC 59.617 50.000 0.00 0.00 46.97 4.01
639 662 0.239347 AACTGCACAAGCGCTGAATC 59.761 50.000 12.58 1.31 46.23 2.52
645 668 1.098050 ACAAGCGCTGAATCCCAATC 58.902 50.000 12.58 0.00 0.00 2.67
708 731 2.354103 CGGTGTGGATGAGACTGTCAAT 60.354 50.000 10.88 3.15 39.19 2.57
709 732 3.005554 GGTGTGGATGAGACTGTCAATG 58.994 50.000 10.88 0.00 39.19 2.82
710 733 2.417933 GTGTGGATGAGACTGTCAATGC 59.582 50.000 10.88 8.99 39.19 3.56
713 736 1.669779 GGATGAGACTGTCAATGCAGC 59.330 52.381 10.88 5.31 39.19 5.25
743 767 3.564511 TCGTACTAGGTTGCGTACAAAC 58.435 45.455 0.00 0.00 44.30 2.93
783 809 0.298707 GTCAGACATGCATGCGTACG 59.701 55.000 26.53 11.84 0.00 3.67
785 811 1.133407 TCAGACATGCATGCGTACGTA 59.867 47.619 26.53 13.65 0.00 3.57
786 812 1.255342 CAGACATGCATGCGTACGTAC 59.745 52.381 26.53 15.90 0.00 3.67
787 813 1.134367 AGACATGCATGCGTACGTACT 59.866 47.619 26.53 3.28 0.00 2.73
788 814 1.924524 GACATGCATGCGTACGTACTT 59.075 47.619 26.53 2.47 0.00 2.24
789 815 3.110358 GACATGCATGCGTACGTACTTA 58.890 45.455 26.53 11.99 0.00 2.24
811 837 2.437200 GCAGCCTGCATGTAAACAAA 57.563 45.000 12.82 0.00 44.26 2.83
816 842 2.927871 GCCTGCATGTAAACAAAGGCAG 60.928 50.000 21.01 20.25 44.08 4.85
818 844 3.505680 CCTGCATGTAAACAAAGGCAGTA 59.494 43.478 22.23 1.24 42.62 2.74
919 968 1.822990 GTCCCGGCGATAGATCCATTA 59.177 52.381 9.30 0.00 39.76 1.90
921 970 3.104512 TCCCGGCGATAGATCCATTAAT 58.895 45.455 9.30 0.00 39.76 1.40
922 971 4.098960 GTCCCGGCGATAGATCCATTAATA 59.901 45.833 9.30 0.00 39.76 0.98
923 972 4.712829 TCCCGGCGATAGATCCATTAATAA 59.287 41.667 9.30 0.00 39.76 1.40
924 973 4.809426 CCCGGCGATAGATCCATTAATAAC 59.191 45.833 9.30 0.00 39.76 1.89
928 977 6.473778 CGGCGATAGATCCATTAATAACTCTG 59.526 42.308 0.00 0.00 39.76 3.35
935 984 8.484214 AGATCCATTAATAACTCTGTGCTAGA 57.516 34.615 0.00 0.00 0.00 2.43
955 1004 1.134670 AGCTCATAAACCGCAGACTCC 60.135 52.381 0.00 0.00 0.00 3.85
956 1005 1.941325 CTCATAAACCGCAGACTCCC 58.059 55.000 0.00 0.00 0.00 4.30
957 1006 0.539986 TCATAAACCGCAGACTCCCC 59.460 55.000 0.00 0.00 0.00 4.81
958 1007 0.463833 CATAAACCGCAGACTCCCCC 60.464 60.000 0.00 0.00 0.00 5.40
959 1008 1.968050 ATAAACCGCAGACTCCCCCG 61.968 60.000 0.00 0.00 0.00 5.73
986 1035 2.649257 GCTATAGACAAGCGCGCGG 61.649 63.158 33.06 24.02 0.00 6.46
1188 1237 1.814169 GTTCAGATTCGGGCCGGTC 60.814 63.158 27.98 23.20 0.00 4.79
1240 1289 3.559024 ACGTGAGTCGATCGTCGT 58.441 55.556 15.94 15.06 44.19 4.34
1241 1290 1.419143 ACGTGAGTCGATCGTCGTC 59.581 57.895 15.94 10.63 44.19 4.20
1251 1300 2.032290 TCGATCGTCGTCATGTCATACC 60.032 50.000 15.94 0.00 41.35 2.73
1253 1302 3.185797 CGATCGTCGTCATGTCATACCTA 59.814 47.826 7.03 0.00 34.72 3.08
1254 1303 3.957671 TCGTCGTCATGTCATACCTAC 57.042 47.619 0.00 0.00 0.00 3.18
1270 1319 0.537828 CTACCTCCTCTCCTACGGGC 60.538 65.000 0.00 0.00 0.00 6.13
1279 1328 4.527038 TCCTCTCCTACGGGCATTAATAAG 59.473 45.833 0.00 0.00 0.00 1.73
1303 1352 4.151417 CGTTGGTACGTACGGTGG 57.849 61.111 21.06 5.48 42.72 4.61
1309 1358 4.611355 CGTTGGTACGTACGGTGGATATAG 60.611 50.000 21.06 0.00 42.72 1.31
1322 1371 5.010719 CGGTGGATATAGTAACATGGACTGT 59.989 44.000 11.67 8.24 40.84 3.55
1333 1382 5.571784 AACATGGACTGTTGATGCTTATG 57.428 39.130 0.00 0.00 46.37 1.90
1343 1392 1.843206 TGATGCTTATGGTGTGCCCTA 59.157 47.619 0.00 0.00 0.00 3.53
1500 1549 4.256110 TGCTTGATGTGGTGAGTATCTTG 58.744 43.478 0.00 0.00 34.92 3.02
1501 1550 4.256920 GCTTGATGTGGTGAGTATCTTGT 58.743 43.478 0.00 0.00 34.92 3.16
1502 1551 5.046663 TGCTTGATGTGGTGAGTATCTTGTA 60.047 40.000 0.00 0.00 34.92 2.41
1503 1552 5.292101 GCTTGATGTGGTGAGTATCTTGTAC 59.708 44.000 0.00 0.00 34.92 2.90
1504 1553 5.993748 TGATGTGGTGAGTATCTTGTACA 57.006 39.130 0.00 0.00 34.92 2.90
1505 1554 6.544928 TGATGTGGTGAGTATCTTGTACAT 57.455 37.500 0.00 0.00 34.92 2.29
1506 1555 6.340522 TGATGTGGTGAGTATCTTGTACATG 58.659 40.000 0.00 0.00 34.92 3.21
1507 1556 5.993748 TGTGGTGAGTATCTTGTACATGA 57.006 39.130 13.28 13.28 34.92 3.07
1508 1557 6.353404 TGTGGTGAGTATCTTGTACATGAA 57.647 37.500 14.70 3.27 34.92 2.57
1509 1558 6.163476 TGTGGTGAGTATCTTGTACATGAAC 58.837 40.000 14.70 13.20 34.92 3.18
1510 1559 6.014584 TGTGGTGAGTATCTTGTACATGAACT 60.015 38.462 14.70 16.72 34.92 3.01
1511 1560 7.177744 TGTGGTGAGTATCTTGTACATGAACTA 59.822 37.037 14.70 4.44 34.92 2.24
1541 1590 6.638096 TGAATGAATTGTTCTCACATGTGT 57.362 33.333 24.63 3.26 31.06 3.72
1545 1597 6.785488 TGAATTGTTCTCACATGTGTAGTC 57.215 37.500 24.63 14.28 31.06 2.59
1546 1598 6.287525 TGAATTGTTCTCACATGTGTAGTCA 58.712 36.000 24.63 16.38 31.06 3.41
1560 1632 9.197306 ACATGTGTAGTCACTAACAATCCTATA 57.803 33.333 0.00 0.00 44.14 1.31
1747 1819 1.599240 GGCCTCATCGCTTCCATCC 60.599 63.158 0.00 0.00 0.00 3.51
1870 1942 0.177141 ATTTCATGTGCCCTGCATGC 59.823 50.000 11.82 11.82 41.91 4.06
1898 1970 1.741525 GCTTTGGTGAGCTTTGCCA 59.258 52.632 0.00 0.00 39.57 4.92
2090 2178 0.519961 GTTTGGAACGATTGGACCCG 59.480 55.000 0.00 0.00 0.00 5.28
2134 2228 0.874175 TTTGCTATCGCCATCGTCCG 60.874 55.000 0.00 0.00 36.96 4.79
2157 2251 4.031028 CGACGGTAGGATTTAACGTACTG 58.969 47.826 0.00 0.00 40.82 2.74
2191 2285 1.152383 GGCGGTAGAAATCTGGTCGC 61.152 60.000 14.12 14.12 38.34 5.19
2241 2335 4.941873 AGTGGCTAGCACATTAAAACCTAC 59.058 41.667 18.24 0.00 0.00 3.18
2268 2362 1.079127 CCTTGGCGGTAGACACCTG 60.079 63.158 0.00 0.00 43.33 4.00
2269 2363 1.541310 CCTTGGCGGTAGACACCTGA 61.541 60.000 0.00 0.00 43.33 3.86
2327 2421 3.436700 GCATGTAACCCTATTGCCAAC 57.563 47.619 0.00 0.00 0.00 3.77
2357 2451 4.202295 GGCGGTAGGGTACTAAATTTAGCT 60.202 45.833 22.45 14.45 34.09 3.32
2396 2490 1.144969 CTCGTGCGTTTCTTTAGGCA 58.855 50.000 0.00 0.00 36.65 4.75
2487 2637 4.456911 ACCATTCTGACTAGCACACAATTG 59.543 41.667 3.24 3.24 0.00 2.32
2488 2638 4.696877 CCATTCTGACTAGCACACAATTGA 59.303 41.667 13.59 0.00 0.00 2.57
2489 2639 5.391310 CCATTCTGACTAGCACACAATTGAC 60.391 44.000 13.59 0.00 0.00 3.18
2490 2640 4.335400 TCTGACTAGCACACAATTGACA 57.665 40.909 13.59 0.00 0.00 3.58
2491 2641 4.898320 TCTGACTAGCACACAATTGACAT 58.102 39.130 13.59 0.00 0.00 3.06
2492 2642 4.931601 TCTGACTAGCACACAATTGACATC 59.068 41.667 13.59 0.00 0.00 3.06
2493 2643 4.640364 TGACTAGCACACAATTGACATCA 58.360 39.130 13.59 1.70 0.00 3.07
2494 2644 5.062528 TGACTAGCACACAATTGACATCAA 58.937 37.500 13.59 0.00 40.51 2.57
2495 2645 5.530543 TGACTAGCACACAATTGACATCAAA 59.469 36.000 13.59 0.00 39.55 2.69
2496 2646 6.207221 TGACTAGCACACAATTGACATCAAAT 59.793 34.615 13.59 0.00 39.55 2.32
2497 2647 7.390162 TGACTAGCACACAATTGACATCAAATA 59.610 33.333 13.59 0.00 39.55 1.40
2498 2648 8.109705 ACTAGCACACAATTGACATCAAATAA 57.890 30.769 13.59 0.00 39.55 1.40
2499 2649 8.023128 ACTAGCACACAATTGACATCAAATAAC 58.977 33.333 13.59 0.00 39.55 1.89
2500 2650 6.747125 AGCACACAATTGACATCAAATAACA 58.253 32.000 13.59 0.00 39.55 2.41
2501 2651 7.208777 AGCACACAATTGACATCAAATAACAA 58.791 30.769 13.59 0.00 39.55 2.83
2502 2652 7.874016 AGCACACAATTGACATCAAATAACAAT 59.126 29.630 13.59 0.00 39.55 2.71
2503 2653 9.138062 GCACACAATTGACATCAAATAACAATA 57.862 29.630 13.59 0.00 39.55 1.90
2579 2729 3.318839 CCACACAACAATTGTCCATCACT 59.681 43.478 12.39 0.00 43.23 3.41
2693 2899 6.555315 CAAGCAAGTGTCCATATTACTTTCC 58.445 40.000 0.00 0.00 32.69 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.775856 CCGAGAGCGCCTAGAGCAA 61.776 63.158 2.29 0.00 44.04 3.91
1 2 3.212682 CCGAGAGCGCCTAGAGCA 61.213 66.667 2.29 0.00 44.04 4.26
2 3 3.189010 GACCGAGAGCGCCTAGAGC 62.189 68.421 2.29 0.00 35.83 4.09
3 4 2.887889 CGACCGAGAGCGCCTAGAG 61.888 68.421 2.29 0.00 35.83 2.43
4 5 2.895865 CGACCGAGAGCGCCTAGA 60.896 66.667 2.29 0.00 35.83 2.43
5 6 2.887889 CTCGACCGAGAGCGCCTAG 61.888 68.421 13.64 0.98 44.53 3.02
21 22 4.387256 CGGAAGACACAAAGAGAACATCTC 59.613 45.833 0.00 0.00 43.70 2.75
22 23 4.310769 CGGAAGACACAAAGAGAACATCT 58.689 43.478 0.00 0.00 41.27 2.90
23 24 3.120511 GCGGAAGACACAAAGAGAACATC 60.121 47.826 0.00 0.00 0.00 3.06
24 25 2.808543 GCGGAAGACACAAAGAGAACAT 59.191 45.455 0.00 0.00 0.00 2.71
25 26 2.158957 AGCGGAAGACACAAAGAGAACA 60.159 45.455 0.00 0.00 0.00 3.18
26 27 2.221981 CAGCGGAAGACACAAAGAGAAC 59.778 50.000 0.00 0.00 0.00 3.01
27 28 2.102420 TCAGCGGAAGACACAAAGAGAA 59.898 45.455 0.00 0.00 0.00 2.87
28 29 1.686587 TCAGCGGAAGACACAAAGAGA 59.313 47.619 0.00 0.00 0.00 3.10
29 30 2.154854 TCAGCGGAAGACACAAAGAG 57.845 50.000 0.00 0.00 0.00 2.85
30 31 2.037121 TGATCAGCGGAAGACACAAAGA 59.963 45.455 0.00 0.00 0.00 2.52
31 32 2.416747 TGATCAGCGGAAGACACAAAG 58.583 47.619 0.00 0.00 0.00 2.77
32 33 2.542020 TGATCAGCGGAAGACACAAA 57.458 45.000 0.00 0.00 0.00 2.83
33 34 2.224281 ACTTGATCAGCGGAAGACACAA 60.224 45.455 0.00 0.00 0.00 3.33
34 35 1.344438 ACTTGATCAGCGGAAGACACA 59.656 47.619 0.00 0.00 0.00 3.72
35 36 2.086054 ACTTGATCAGCGGAAGACAC 57.914 50.000 0.00 0.00 0.00 3.67
36 37 2.839486 AACTTGATCAGCGGAAGACA 57.161 45.000 0.00 0.00 0.00 3.41
37 38 3.851098 AGTAACTTGATCAGCGGAAGAC 58.149 45.455 0.00 0.00 0.00 3.01
38 39 5.394224 CCTTAGTAACTTGATCAGCGGAAGA 60.394 44.000 0.00 0.00 0.00 2.87
39 40 4.806247 CCTTAGTAACTTGATCAGCGGAAG 59.194 45.833 0.00 0.00 0.00 3.46
40 41 4.464951 TCCTTAGTAACTTGATCAGCGGAA 59.535 41.667 0.00 0.00 0.00 4.30
41 42 4.021229 TCCTTAGTAACTTGATCAGCGGA 58.979 43.478 0.00 0.00 0.00 5.54
42 43 4.386867 TCCTTAGTAACTTGATCAGCGG 57.613 45.455 0.00 0.00 0.00 5.52
43 44 6.910536 AAATCCTTAGTAACTTGATCAGCG 57.089 37.500 0.00 0.00 0.00 5.18
44 45 8.821894 CAGTAAATCCTTAGTAACTTGATCAGC 58.178 37.037 0.00 0.00 0.00 4.26
45 46 9.877178 ACAGTAAATCCTTAGTAACTTGATCAG 57.123 33.333 0.00 0.00 0.00 2.90
53 54 9.070149 CGTTCAGTACAGTAAATCCTTAGTAAC 57.930 37.037 0.00 0.00 0.00 2.50
54 55 9.013229 TCGTTCAGTACAGTAAATCCTTAGTAA 57.987 33.333 0.00 0.00 0.00 2.24
55 56 8.565896 TCGTTCAGTACAGTAAATCCTTAGTA 57.434 34.615 0.00 0.00 0.00 1.82
56 57 7.458409 TCGTTCAGTACAGTAAATCCTTAGT 57.542 36.000 0.00 0.00 0.00 2.24
57 58 6.472808 GCTCGTTCAGTACAGTAAATCCTTAG 59.527 42.308 0.00 0.00 0.00 2.18
58 59 6.071784 TGCTCGTTCAGTACAGTAAATCCTTA 60.072 38.462 0.00 0.00 0.00 2.69
59 60 5.169295 GCTCGTTCAGTACAGTAAATCCTT 58.831 41.667 0.00 0.00 0.00 3.36
60 61 4.219944 TGCTCGTTCAGTACAGTAAATCCT 59.780 41.667 0.00 0.00 0.00 3.24
61 62 4.491676 TGCTCGTTCAGTACAGTAAATCC 58.508 43.478 0.00 0.00 0.00 3.01
62 63 5.634020 AGTTGCTCGTTCAGTACAGTAAATC 59.366 40.000 0.00 0.00 0.00 2.17
63 64 5.539048 AGTTGCTCGTTCAGTACAGTAAAT 58.461 37.500 0.00 0.00 0.00 1.40
64 65 4.940463 AGTTGCTCGTTCAGTACAGTAAA 58.060 39.130 0.00 0.00 0.00 2.01
65 66 4.579454 AGTTGCTCGTTCAGTACAGTAA 57.421 40.909 0.00 0.00 0.00 2.24
66 67 5.335426 CCTTAGTTGCTCGTTCAGTACAGTA 60.335 44.000 0.00 0.00 0.00 2.74
67 68 4.547532 CTTAGTTGCTCGTTCAGTACAGT 58.452 43.478 0.00 0.00 0.00 3.55
68 69 3.921021 CCTTAGTTGCTCGTTCAGTACAG 59.079 47.826 0.00 0.00 0.00 2.74
69 70 3.319972 ACCTTAGTTGCTCGTTCAGTACA 59.680 43.478 0.00 0.00 0.00 2.90
70 71 3.673809 CACCTTAGTTGCTCGTTCAGTAC 59.326 47.826 0.00 0.00 0.00 2.73
71 72 3.570975 TCACCTTAGTTGCTCGTTCAGTA 59.429 43.478 0.00 0.00 0.00 2.74
72 73 2.364324 TCACCTTAGTTGCTCGTTCAGT 59.636 45.455 0.00 0.00 0.00 3.41
73 74 3.026630 TCACCTTAGTTGCTCGTTCAG 57.973 47.619 0.00 0.00 0.00 3.02
74 75 3.325870 CATCACCTTAGTTGCTCGTTCA 58.674 45.455 0.00 0.00 0.00 3.18
75 76 2.094417 GCATCACCTTAGTTGCTCGTTC 59.906 50.000 0.00 0.00 32.78 3.95
76 77 2.076863 GCATCACCTTAGTTGCTCGTT 58.923 47.619 0.00 0.00 32.78 3.85
77 78 1.276421 AGCATCACCTTAGTTGCTCGT 59.724 47.619 0.00 0.00 39.65 4.18
78 79 2.015736 AGCATCACCTTAGTTGCTCG 57.984 50.000 0.00 0.00 39.65 5.03
79 80 2.349886 CGAAGCATCACCTTAGTTGCTC 59.650 50.000 0.00 0.00 42.13 4.26
80 81 2.028112 TCGAAGCATCACCTTAGTTGCT 60.028 45.455 0.00 0.00 44.15 3.91
81 82 2.346803 TCGAAGCATCACCTTAGTTGC 58.653 47.619 0.00 0.00 35.09 4.17
82 83 3.310774 CCATCGAAGCATCACCTTAGTTG 59.689 47.826 0.00 0.00 0.00 3.16
83 84 3.197766 TCCATCGAAGCATCACCTTAGTT 59.802 43.478 0.00 0.00 0.00 2.24
84 85 2.766263 TCCATCGAAGCATCACCTTAGT 59.234 45.455 0.00 0.00 0.00 2.24
85 86 3.459232 TCCATCGAAGCATCACCTTAG 57.541 47.619 0.00 0.00 0.00 2.18
86 87 3.387699 TCATCCATCGAAGCATCACCTTA 59.612 43.478 0.00 0.00 0.00 2.69
87 88 2.171237 TCATCCATCGAAGCATCACCTT 59.829 45.455 0.00 0.00 0.00 3.50
88 89 1.764723 TCATCCATCGAAGCATCACCT 59.235 47.619 0.00 0.00 0.00 4.00
89 90 2.245159 TCATCCATCGAAGCATCACC 57.755 50.000 0.00 0.00 0.00 4.02
90 91 4.388165 CAGTATCATCCATCGAAGCATCAC 59.612 45.833 0.00 0.00 0.00 3.06
91 92 4.039609 ACAGTATCATCCATCGAAGCATCA 59.960 41.667 0.00 0.00 0.00 3.07
92 93 4.564041 ACAGTATCATCCATCGAAGCATC 58.436 43.478 0.00 0.00 0.00 3.91
93 94 4.613925 ACAGTATCATCCATCGAAGCAT 57.386 40.909 0.00 0.00 0.00 3.79
94 95 5.728637 ATACAGTATCATCCATCGAAGCA 57.271 39.130 0.00 0.00 0.00 3.91
95 96 5.163913 GCAATACAGTATCATCCATCGAAGC 60.164 44.000 0.00 0.00 0.00 3.86
96 97 5.349817 GGCAATACAGTATCATCCATCGAAG 59.650 44.000 0.00 0.00 0.00 3.79
97 98 5.221621 TGGCAATACAGTATCATCCATCGAA 60.222 40.000 0.00 0.00 0.00 3.71
98 99 4.283212 TGGCAATACAGTATCATCCATCGA 59.717 41.667 0.00 0.00 0.00 3.59
99 100 4.568956 TGGCAATACAGTATCATCCATCG 58.431 43.478 0.00 0.00 0.00 3.84
100 101 7.458409 AATTGGCAATACAGTATCATCCATC 57.542 36.000 14.05 0.00 0.00 3.51
101 102 8.796475 GTTAATTGGCAATACAGTATCATCCAT 58.204 33.333 14.05 0.00 0.00 3.41
102 103 7.777440 TGTTAATTGGCAATACAGTATCATCCA 59.223 33.333 14.05 0.00 0.00 3.41
103 104 8.165239 TGTTAATTGGCAATACAGTATCATCC 57.835 34.615 14.05 0.00 0.00 3.51
111 112 9.398170 GCTACAATATGTTAATTGGCAATACAG 57.602 33.333 14.05 5.95 40.48 2.74
112 113 8.907885 TGCTACAATATGTTAATTGGCAATACA 58.092 29.630 14.05 15.16 40.48 2.29
113 114 9.912634 ATGCTACAATATGTTAATTGGCAATAC 57.087 29.630 14.05 9.60 40.48 1.89
114 115 9.911138 CATGCTACAATATGTTAATTGGCAATA 57.089 29.630 14.05 0.00 40.48 1.90
115 116 8.640651 TCATGCTACAATATGTTAATTGGCAAT 58.359 29.630 6.96 6.96 40.48 3.56
116 117 7.920151 GTCATGCTACAATATGTTAATTGGCAA 59.080 33.333 0.68 0.68 40.48 4.52
117 118 7.424803 GTCATGCTACAATATGTTAATTGGCA 58.575 34.615 2.05 3.11 40.48 4.92
118 119 6.863126 GGTCATGCTACAATATGTTAATTGGC 59.137 38.462 2.05 0.00 40.48 4.52
119 120 7.939782 TGGTCATGCTACAATATGTTAATTGG 58.060 34.615 2.05 0.00 40.48 3.16
120 121 8.623903 ACTGGTCATGCTACAATATGTTAATTG 58.376 33.333 0.00 0.00 41.65 2.32
200 201 9.817809 CCATATTGGTATTACTAATACAGCGAT 57.182 33.333 17.17 10.27 44.37 4.58
204 205 7.494625 CCGGCCATATTGGTATTACTAATACAG 59.505 40.741 17.17 9.47 44.37 2.74
205 206 7.180587 TCCGGCCATATTGGTATTACTAATACA 59.819 37.037 17.17 2.54 44.37 2.29
224 234 3.249189 GCCTATCCCATCCGGCCA 61.249 66.667 2.24 0.00 36.56 5.36
229 239 1.188219 TCGAGCAGCCTATCCCATCC 61.188 60.000 0.00 0.00 0.00 3.51
234 244 2.246719 ATGTTTCGAGCAGCCTATCC 57.753 50.000 0.00 0.00 0.00 2.59
287 304 3.694566 GGGGTTGCTTATCTAGTTTGTGG 59.305 47.826 0.00 0.00 0.00 4.17
332 349 0.250901 ACCATCGCTTTCACTTGCCT 60.251 50.000 0.00 0.00 0.00 4.75
336 353 1.317613 TGCAACCATCGCTTTCACTT 58.682 45.000 0.00 0.00 0.00 3.16
337 354 1.538047 ATGCAACCATCGCTTTCACT 58.462 45.000 0.00 0.00 0.00 3.41
351 368 2.489329 GCTAGCTGTTCTCCAAATGCAA 59.511 45.455 7.70 0.00 0.00 4.08
406 423 1.018148 TTGTACACCAGTTGCGGTTG 58.982 50.000 0.00 0.00 37.07 3.77
407 424 1.018910 GTTGTACACCAGTTGCGGTT 58.981 50.000 0.00 0.00 37.07 4.44
408 425 0.179468 AGTTGTACACCAGTTGCGGT 59.821 50.000 0.00 0.00 41.07 5.68
409 426 1.263217 GAAGTTGTACACCAGTTGCGG 59.737 52.381 0.00 0.00 0.00 5.69
410 427 1.263217 GGAAGTTGTACACCAGTTGCG 59.737 52.381 0.00 0.00 0.00 4.85
411 428 2.294074 TGGAAGTTGTACACCAGTTGC 58.706 47.619 0.00 0.00 0.00 4.17
440 457 0.036732 GGAAGCTGACATCCACACCA 59.963 55.000 0.00 0.00 33.69 4.17
444 461 1.028868 GCAGGGAAGCTGACATCCAC 61.029 60.000 4.59 0.00 35.26 4.02
454 477 0.106708 TGTGATATCGGCAGGGAAGC 59.893 55.000 0.00 0.00 0.00 3.86
462 485 4.119862 AGTACATTGTGTGTGATATCGGC 58.880 43.478 0.00 0.00 42.24 5.54
466 489 5.163301 GGAGGGAGTACATTGTGTGTGATAT 60.163 44.000 0.00 0.00 42.24 1.63
483 506 3.629142 AGTAATTCCAAACGGAGGGAG 57.371 47.619 0.00 0.00 34.02 4.30
484 507 3.073356 ACAAGTAATTCCAAACGGAGGGA 59.927 43.478 0.00 0.00 32.88 4.20
485 508 3.418047 ACAAGTAATTCCAAACGGAGGG 58.582 45.455 0.00 0.00 32.88 4.30
486 509 4.069304 TGACAAGTAATTCCAAACGGAGG 58.931 43.478 0.00 0.00 32.88 4.30
487 510 5.880054 ATGACAAGTAATTCCAAACGGAG 57.120 39.130 0.00 0.00 32.88 4.63
488 511 7.747155 TTTATGACAAGTAATTCCAAACGGA 57.253 32.000 0.00 0.00 0.00 4.69
489 512 8.804688 TTTTTATGACAAGTAATTCCAAACGG 57.195 30.769 0.00 0.00 0.00 4.44
581 604 5.701750 TCCGTTCGGAATTACTCATCAAAAA 59.298 36.000 11.66 0.00 0.00 1.94
582 605 5.239351 TCCGTTCGGAATTACTCATCAAAA 58.761 37.500 11.66 0.00 0.00 2.44
583 606 4.823157 TCCGTTCGGAATTACTCATCAAA 58.177 39.130 11.66 0.00 0.00 2.69
584 607 4.430007 CTCCGTTCGGAATTACTCATCAA 58.570 43.478 14.79 0.00 33.41 2.57
585 608 3.181479 CCTCCGTTCGGAATTACTCATCA 60.181 47.826 14.79 0.00 33.41 3.07
586 609 3.381949 CCTCCGTTCGGAATTACTCATC 58.618 50.000 14.79 0.00 33.41 2.92
587 610 2.102588 CCCTCCGTTCGGAATTACTCAT 59.897 50.000 14.79 0.00 33.41 2.90
588 611 1.479323 CCCTCCGTTCGGAATTACTCA 59.521 52.381 14.79 0.00 33.41 3.41
589 612 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
590 613 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
591 614 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
592 615 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
593 616 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
594 617 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
595 618 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
596 619 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
597 620 0.739561 CTTCTACTCCCTCCGTTCGG 59.260 60.000 4.74 4.74 0.00 4.30
598 621 0.100861 GCTTCTACTCCCTCCGTTCG 59.899 60.000 0.00 0.00 0.00 3.95
599 622 1.135053 GTGCTTCTACTCCCTCCGTTC 60.135 57.143 0.00 0.00 0.00 3.95
600 623 0.896226 GTGCTTCTACTCCCTCCGTT 59.104 55.000 0.00 0.00 0.00 4.44
601 624 0.251653 TGTGCTTCTACTCCCTCCGT 60.252 55.000 0.00 0.00 0.00 4.69
602 625 0.895530 TTGTGCTTCTACTCCCTCCG 59.104 55.000 0.00 0.00 0.00 4.63
603 626 1.903183 AGTTGTGCTTCTACTCCCTCC 59.097 52.381 0.00 0.00 0.00 4.30
604 627 2.966050 CAGTTGTGCTTCTACTCCCTC 58.034 52.381 0.00 0.00 30.39 4.30
617 640 1.656263 CAGCGCTTGTGCAGTTGTG 60.656 57.895 7.50 0.00 39.64 3.33
618 641 1.375853 TTCAGCGCTTGTGCAGTTGT 61.376 50.000 7.50 0.00 39.64 3.32
619 642 0.039798 ATTCAGCGCTTGTGCAGTTG 60.040 50.000 7.50 0.00 39.64 3.16
620 643 0.239347 GATTCAGCGCTTGTGCAGTT 59.761 50.000 7.50 0.00 39.64 3.16
621 644 1.580845 GGATTCAGCGCTTGTGCAGT 61.581 55.000 7.50 0.00 39.64 4.40
622 645 1.136147 GGATTCAGCGCTTGTGCAG 59.864 57.895 7.50 0.00 39.64 4.41
623 646 2.334946 GGGATTCAGCGCTTGTGCA 61.335 57.895 7.50 0.00 39.64 4.57
631 654 0.378257 CCGTTGATTGGGATTCAGCG 59.622 55.000 3.41 3.41 44.28 5.18
639 662 1.361668 CGTGCTCTCCGTTGATTGGG 61.362 60.000 0.00 0.00 0.00 4.12
645 668 0.874175 TGTTCACGTGCTCTCCGTTG 60.874 55.000 11.67 0.00 36.17 4.10
668 691 1.917303 CGCGAATATGTTTGGGTTTGC 59.083 47.619 0.00 0.00 0.00 3.68
730 753 2.948323 CCCGGTTTGTACGCAACC 59.052 61.111 14.27 14.27 33.82 3.77
743 767 2.754946 TTGACTTGTAAGTAGCCCGG 57.245 50.000 0.00 0.00 39.88 5.73
783 809 1.667724 CATGCAGGCTGCTGTAAGTAC 59.332 52.381 36.50 8.46 45.31 2.73
785 811 0.037303 ACATGCAGGCTGCTGTAAGT 59.963 50.000 36.50 23.95 45.31 2.24
786 812 2.028420 TACATGCAGGCTGCTGTAAG 57.972 50.000 36.50 23.37 45.31 2.34
787 813 2.487762 GTTTACATGCAGGCTGCTGTAA 59.512 45.455 34.71 34.71 45.31 2.41
788 814 2.083774 GTTTACATGCAGGCTGCTGTA 58.916 47.619 36.50 32.89 45.31 2.74
789 815 0.883833 GTTTACATGCAGGCTGCTGT 59.116 50.000 36.50 33.78 45.31 4.40
801 827 4.320202 CGCTGTTACTGCCTTTGTTTACAT 60.320 41.667 8.57 0.00 0.00 2.29
811 837 0.606401 AATGCACGCTGTTACTGCCT 60.606 50.000 8.57 0.00 0.00 4.75
816 842 2.510615 GTGAGAATGCACGCTGTTAC 57.489 50.000 0.00 0.00 0.00 2.50
910 959 8.484214 TCTAGCACAGAGTTATTAATGGATCT 57.516 34.615 0.00 0.00 0.00 2.75
911 960 8.755696 CTCTAGCACAGAGTTATTAATGGATC 57.244 38.462 0.00 0.00 45.10 3.36
928 977 1.861575 GCGGTTTATGAGCTCTAGCAC 59.138 52.381 16.19 6.70 45.16 4.40
935 984 1.134670 GGAGTCTGCGGTTTATGAGCT 60.135 52.381 0.00 0.00 0.00 4.09
941 990 2.652095 CGGGGGAGTCTGCGGTTTA 61.652 63.158 0.00 0.00 0.00 2.01
957 1006 4.379243 CTATAGCTGGGCGGGCGG 62.379 72.222 0.00 0.00 34.52 6.13
958 1007 3.303135 TCTATAGCTGGGCGGGCG 61.303 66.667 0.00 0.00 34.52 6.13
959 1008 2.040009 TTGTCTATAGCTGGGCGGGC 62.040 60.000 0.00 0.00 0.00 6.13
1188 1237 1.971695 GTCTTTGAACTGGGCGGGG 60.972 63.158 0.00 0.00 0.00 5.73
1240 1289 4.447908 GGAGAGGAGGTAGGTATGACATGA 60.448 50.000 0.00 0.00 0.00 3.07
1241 1290 3.829601 GGAGAGGAGGTAGGTATGACATG 59.170 52.174 0.00 0.00 0.00 3.21
1270 1319 5.560966 ACCAACGTGGAAGCTTATTAATG 57.439 39.130 0.00 0.00 40.96 1.90
1295 1344 6.208204 AGTCCATGTTACTATATCCACCGTAC 59.792 42.308 0.00 0.00 0.00 3.67
1296 1345 6.208007 CAGTCCATGTTACTATATCCACCGTA 59.792 42.308 0.00 0.00 0.00 4.02
1297 1346 5.010719 CAGTCCATGTTACTATATCCACCGT 59.989 44.000 0.00 0.00 0.00 4.83
1298 1347 5.010719 ACAGTCCATGTTACTATATCCACCG 59.989 44.000 0.00 0.00 39.96 4.94
1322 1371 1.005805 AGGGCACACCATAAGCATCAA 59.994 47.619 0.00 0.00 43.89 2.57
1333 1382 0.822164 ACACGTAGATAGGGCACACC 59.178 55.000 0.00 0.00 40.67 4.16
1343 1392 2.543777 ACTGCAAACCACACGTAGAT 57.456 45.000 0.00 0.00 0.00 1.98
1500 1549 8.997621 TTCATTCAAGGTAGTAGTTCATGTAC 57.002 34.615 0.00 0.00 0.00 2.90
1502 1551 8.950210 CAATTCATTCAAGGTAGTAGTTCATGT 58.050 33.333 0.00 0.00 0.00 3.21
1503 1552 8.950210 ACAATTCATTCAAGGTAGTAGTTCATG 58.050 33.333 0.00 0.00 0.00 3.07
1504 1553 9.520515 AACAATTCATTCAAGGTAGTAGTTCAT 57.479 29.630 0.00 0.00 0.00 2.57
1505 1554 8.918202 AACAATTCATTCAAGGTAGTAGTTCA 57.082 30.769 0.00 0.00 0.00 3.18
1506 1555 9.220767 AGAACAATTCATTCAAGGTAGTAGTTC 57.779 33.333 0.00 0.00 0.00 3.01
1507 1556 9.220767 GAGAACAATTCATTCAAGGTAGTAGTT 57.779 33.333 2.61 0.00 0.00 2.24
1508 1557 8.375506 TGAGAACAATTCATTCAAGGTAGTAGT 58.624 33.333 2.61 0.00 0.00 2.73
1509 1558 8.660373 GTGAGAACAATTCATTCAAGGTAGTAG 58.340 37.037 2.61 0.00 0.00 2.57
1510 1559 8.154203 TGTGAGAACAATTCATTCAAGGTAGTA 58.846 33.333 2.61 0.00 0.00 1.82
1511 1560 6.998074 TGTGAGAACAATTCATTCAAGGTAGT 59.002 34.615 2.61 0.00 0.00 2.73
1568 1640 3.558418 CGCGTAAACCTGCCATAGTTAAT 59.442 43.478 0.00 0.00 0.00 1.40
1569 1641 2.931325 CGCGTAAACCTGCCATAGTTAA 59.069 45.455 0.00 0.00 0.00 2.01
1570 1642 2.542597 CGCGTAAACCTGCCATAGTTA 58.457 47.619 0.00 0.00 0.00 2.24
1571 1643 1.365699 CGCGTAAACCTGCCATAGTT 58.634 50.000 0.00 0.00 0.00 2.24
1572 1644 0.461339 CCGCGTAAACCTGCCATAGT 60.461 55.000 4.92 0.00 0.00 2.12
1573 1645 1.157870 CCCGCGTAAACCTGCCATAG 61.158 60.000 4.92 0.00 0.00 2.23
1574 1646 1.153329 CCCGCGTAAACCTGCCATA 60.153 57.895 4.92 0.00 0.00 2.74
1740 1812 0.397254 GGAGGACGAGGAGGATGGAA 60.397 60.000 0.00 0.00 0.00 3.53
1747 1819 2.174969 CGACGAGGAGGACGAGGAG 61.175 68.421 0.00 0.00 34.70 3.69
1825 1897 3.382832 CCAGCCGGACGAAGGAGT 61.383 66.667 5.05 0.00 0.00 3.85
1850 1922 1.409790 GCATGCAGGGCACATGAAATA 59.590 47.619 14.21 0.00 46.33 1.40
1870 1942 2.046314 ACCAAAGCCGACGGATGG 60.046 61.111 20.50 22.77 37.19 3.51
1898 1970 1.324740 TATACAACTGACCGCCCGCT 61.325 55.000 0.00 0.00 0.00 5.52
1901 1973 3.602483 TCTTTTATACAACTGACCGCCC 58.398 45.455 0.00 0.00 0.00 6.13
2102 2196 4.282068 CGATAGCAAATGGTCAAATTCGG 58.718 43.478 0.00 0.00 0.00 4.30
2134 2228 1.913317 ACGTTAAATCCTACCGTCGC 58.087 50.000 0.00 0.00 0.00 5.19
2136 2230 3.793492 GCAGTACGTTAAATCCTACCGTC 59.207 47.826 0.00 0.00 33.32 4.79
2137 2231 3.429410 GGCAGTACGTTAAATCCTACCGT 60.429 47.826 0.00 0.00 35.68 4.83
2191 2285 0.855349 GTCAACGAGTGCTGTGACAG 59.145 55.000 8.52 8.52 34.12 3.51
2268 2362 1.475213 CCCCAATCTCTTACCCGCTTC 60.475 57.143 0.00 0.00 0.00 3.86
2269 2363 0.546598 CCCCAATCTCTTACCCGCTT 59.453 55.000 0.00 0.00 0.00 4.68
2327 2421 0.595095 GTACCCTACCGCCATAGACG 59.405 60.000 0.00 0.00 0.00 4.18
2357 2451 4.505191 CGAGAACTTTCAGTACCGTTTTGA 59.495 41.667 0.00 0.00 0.00 2.69
2382 2476 2.007608 CCCTACTGCCTAAAGAAACGC 58.992 52.381 0.00 0.00 0.00 4.84
2529 2679 9.953697 GGAATTTAAATGTTATGGTTATACGCA 57.046 29.630 0.39 0.00 0.00 5.24
2530 2680 9.953697 TGGAATTTAAATGTTATGGTTATACGC 57.046 29.630 0.39 0.00 0.00 4.42
2535 2685 9.090103 TGTGGTGGAATTTAAATGTTATGGTTA 57.910 29.630 0.39 0.00 0.00 2.85
2536 2686 7.875554 GTGTGGTGGAATTTAAATGTTATGGTT 59.124 33.333 0.39 0.00 0.00 3.67
2537 2687 7.015682 TGTGTGGTGGAATTTAAATGTTATGGT 59.984 33.333 0.39 0.00 0.00 3.55
2538 2688 7.382110 TGTGTGGTGGAATTTAAATGTTATGG 58.618 34.615 0.39 0.00 0.00 2.74
2539 2689 8.707839 GTTGTGTGGTGGAATTTAAATGTTATG 58.292 33.333 0.39 0.00 0.00 1.90
2540 2690 8.424918 TGTTGTGTGGTGGAATTTAAATGTTAT 58.575 29.630 0.39 0.00 0.00 1.89
2541 2691 7.782049 TGTTGTGTGGTGGAATTTAAATGTTA 58.218 30.769 0.39 0.00 0.00 2.41
2548 2698 6.227298 ACAATTGTTGTGTGGTGGAATTTA 57.773 33.333 4.92 0.00 43.48 1.40
2693 2899 1.475403 TCGTCTAAGCAAGAGGGGAG 58.525 55.000 8.40 0.00 39.97 4.30


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

AutoCloner maintained by Alex Coulton.