Multiple sequence alignment - TraesCS5D01G209300

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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 TraesCS5D01G209300 chr5D 100.000 8005 0 0 1 8005 315938888 315930884 0.000000e+00 14783
1 TraesCS5D01G209300 chr5D 84.007 594 77 8 3 583 377160688 377161276 9.080000e-154 555
2 TraesCS5D01G209300 chr5D 88.716 257 26 3 2658 2913 287806768 287807022 2.170000e-80 311
3 TraesCS5D01G209300 chr5A 96.064 3023 83 18 5005 8005 410509895 410506887 0.000000e+00 4891
4 TraesCS5D01G209300 chr5A 92.563 2259 109 18 749 3001 410514956 410512751 0.000000e+00 3186
5 TraesCS5D01G209300 chr5A 92.849 895 50 6 3737 4624 410511349 410510462 0.000000e+00 1286
6 TraesCS5D01G209300 chr5A 93.159 687 32 2 3014 3696 410512024 410511349 0.000000e+00 994
7 TraesCS5D01G209300 chr5A 95.385 130 4 1 4621 4748 410510302 410510173 1.050000e-48 206
8 TraesCS5D01G209300 chr5A 93.519 108 3 2 4903 5006 410510187 410510080 2.990000e-34 158
9 TraesCS5D01G209300 chr5A 97.260 73 2 0 679 751 410515538 410515466 3.030000e-24 124
10 TraesCS5D01G209300 chr5B 92.491 3143 152 37 4903 8005 364137621 364134523 0.000000e+00 4420
11 TraesCS5D01G209300 chr5B 95.482 2280 80 9 679 2943 364141775 364139504 0.000000e+00 3618
12 TraesCS5D01G209300 chr5B 96.311 1816 55 6 2945 4750 364139418 364137605 0.000000e+00 2972
13 TraesCS5D01G209300 chr5B 88.327 257 28 2 2658 2913 326916146 326916401 2.810000e-79 307
14 TraesCS5D01G209300 chr5B 94.194 155 3 5 4779 4931 179222043 179221893 1.740000e-56 231
15 TraesCS5D01G209300 chr5B 94.444 144 7 1 4776 4918 601402876 601403019 3.760000e-53 220
16 TraesCS5D01G209300 chr3A 83.186 678 93 8 2 664 212303844 212303173 1.150000e-167 601
17 TraesCS5D01G209300 chr1B 84.946 558 58 9 1 558 195047382 195046851 7.070000e-150 542
18 TraesCS5D01G209300 chr2B 82.466 519 66 10 130 627 443458686 443459200 1.600000e-116 431
19 TraesCS5D01G209300 chr4A 88.446 251 29 0 2658 2908 312683427 312683177 3.630000e-78 303
20 TraesCS5D01G209300 chr4B 87.500 248 31 0 2658 2905 317763289 317763536 3.660000e-73 287
21 TraesCS5D01G209300 chr3D 85.115 262 37 2 2655 2915 335667235 335667495 4.760000e-67 267
22 TraesCS5D01G209300 chr1D 84.351 262 34 5 2660 2916 63609355 63609096 4.800000e-62 250
23 TraesCS5D01G209300 chr1A 83.969 262 38 3 2656 2916 508735137 508734879 1.730000e-61 248
24 TraesCS5D01G209300 chr7B 97.744 133 1 2 4779 4909 401536907 401536775 2.250000e-55 228
25 TraesCS5D01G209300 chr6B 97.744 133 1 2 4779 4909 358303156 358303024 2.250000e-55 228
26 TraesCS5D01G209300 chr6B 92.857 154 8 3 4776 4926 433045140 433045293 3.760000e-53 220
27 TraesCS5D01G209300 chr2A 97.744 133 1 2 4779 4909 423846201 423846069 2.250000e-55 228
28 TraesCS5D01G209300 chr2A 95.105 143 4 2 4779 4920 116446043 116445903 1.050000e-53 222
29 TraesCS5D01G209300 chr6D 95.683 139 3 3 4779 4916 83053893 83053757 3.760000e-53 220
30 TraesCS5D01G209300 chr6D 92.857 154 8 3 4751 4902 389581023 389580871 3.760000e-53 220
31 TraesCS5D01G209300 chr6A 94.000 50 2 1 3171 3220 466148690 466148738 3.100000e-09 75
32 TraesCS5D01G209300 chr6A 94.000 50 2 1 3171 3220 466341777 466341825 3.100000e-09 75
33 TraesCS5D01G209300 chr6A 94.000 50 2 1 3171 3220 466359835 466359883 3.100000e-09 75
34 TraesCS5D01G209300 chr6A 94.000 50 2 1 3171 3220 466390998 466391046 3.100000e-09 75


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 TraesCS5D01G209300 chr5D 315930884 315938888 8004 True 14783.000000 14783 100.000000 1 8005 1 chr5D.!!$R1 8004
1 TraesCS5D01G209300 chr5D 377160688 377161276 588 False 555.000000 555 84.007000 3 583 1 chr5D.!!$F2 580
2 TraesCS5D01G209300 chr5A 410506887 410515538 8651 True 1549.285714 4891 94.399857 679 8005 7 chr5A.!!$R1 7326
3 TraesCS5D01G209300 chr5B 364134523 364141775 7252 True 3670.000000 4420 94.761333 679 8005 3 chr5B.!!$R2 7326
4 TraesCS5D01G209300 chr3A 212303173 212303844 671 True 601.000000 601 83.186000 2 664 1 chr3A.!!$R1 662
5 TraesCS5D01G209300 chr1B 195046851 195047382 531 True 542.000000 542 84.946000 1 558 1 chr1B.!!$R1 557
6 TraesCS5D01G209300 chr2B 443458686 443459200 514 False 431.000000 431 82.466000 130 627 1 chr2B.!!$F1 497

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
671 695 0.113580 GGTGGCCCAGGGTCTAAAAA 59.886 55.0 12.68 0.0 0.00 1.94 F
1877 2429 0.250295 TGTTCAGGGCGGTCTCTTTG 60.250 55.0 0.00 0.0 0.00 2.77 F
1878 2430 0.250338 GTTCAGGGCGGTCTCTTTGT 60.250 55.0 0.00 0.0 0.00 2.83 F
3108 4461 0.811616 GGGCCGAGTGCTACTTGATG 60.812 60.0 0.00 0.0 40.92 3.07 F
4294 5655 1.123077 TGACCTCGCCAGCTATTCAT 58.877 50.0 0.00 0.0 0.00 2.57 F
4781 6316 0.032678 CAGTGCACTTCTCGGTGTCT 59.967 55.0 18.94 0.0 39.21 3.41 F
4782 6317 0.032678 AGTGCACTTCTCGGTGTCTG 59.967 55.0 15.25 0.0 39.21 3.51 F
4836 6371 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.0 8.73 0.0 40.08 4.58 F
4842 6377 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.0 0.00 0.0 45.03 3.95 F
4878 6413 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.0 2.00 0.0 31.05 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 3085 1.204467 CCGCCAAGTGCAAACCATAAT 59.796 47.619 0.00 0.00 41.33 1.28 R
3785 5145 0.617413 ACTCCAGGTGCATGAGAAGG 59.383 55.000 0.00 0.00 0.00 3.46 R
3788 5148 1.649321 AAGACTCCAGGTGCATGAGA 58.351 50.000 0.00 0.00 0.00 3.27 R
4762 6297 0.032678 AGACACCGAGAAGTGCACTG 59.967 55.000 22.49 10.04 41.67 3.66 R
5400 7128 2.953466 TCGGTCCAGTATACACAAGC 57.047 50.000 5.50 0.00 0.00 4.01 R
6233 7969 3.505386 ACCATGAAATGTTGCCTGGTTA 58.495 40.909 0.00 0.00 44.81 2.85 R
6602 8339 7.391554 AGGCTAATAATATGCACACACCAATAG 59.608 37.037 0.00 0.00 0.00 1.73 R
6892 8630 6.548622 CCAATAAGATGTGAATCTTCCACCAT 59.451 38.462 4.30 0.00 40.91 3.55 R
6919 8657 1.071894 CACGAGAGCGACATATTTGCG 60.072 52.381 0.00 0.00 40.01 4.85 R
7116 8854 6.073440 ACCATGTACAAAGACAAACGATGTAC 60.073 38.462 0.00 7.28 44.12 2.90 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
47 48 1.300931 GCGCTTCACCTCTGACACA 60.301 57.895 0.00 0.00 0.00 3.72
74 75 2.115052 TGCGCACCCATGGAAACT 59.885 55.556 15.22 0.00 0.00 2.66
89 90 3.010138 TGGAAACTGGTAGAAGGAATGGG 59.990 47.826 0.00 0.00 0.00 4.00
90 91 3.265995 GGAAACTGGTAGAAGGAATGGGA 59.734 47.826 0.00 0.00 0.00 4.37
94 95 0.474614 GGTAGAAGGAATGGGAGGGC 59.525 60.000 0.00 0.00 0.00 5.19
110 114 4.811364 GCCAAGCAGGAGGAGGGC 62.811 72.222 0.00 0.00 41.22 5.19
111 115 3.333219 CCAAGCAGGAGGAGGGCA 61.333 66.667 0.00 0.00 41.22 5.36
177 181 0.392336 GGTCTGCAGCCTGATAGAGG 59.608 60.000 9.47 0.00 46.13 3.69
265 280 6.148270 CGTCTAAAGATCAAAGTAACGCAA 57.852 37.500 0.00 0.00 0.00 4.85
267 282 6.346279 CGTCTAAAGATCAAAGTAACGCAACA 60.346 38.462 0.00 0.00 0.00 3.33
270 285 4.992381 AGATCAAAGTAACGCAACAGTC 57.008 40.909 0.00 0.00 0.00 3.51
306 321 1.267806 CTGGCAGTCAAAAGCGACAAT 59.732 47.619 6.28 0.00 38.43 2.71
393 408 1.605232 CCTAACCAAAACCCGTGACAC 59.395 52.381 0.00 0.00 0.00 3.67
396 411 1.454111 CCAAAACCCGTGACACCCA 60.454 57.895 0.00 0.00 0.00 4.51
431 446 6.679392 GCACACCATATTTATAGGCGTTTGTT 60.679 38.462 0.00 0.00 0.00 2.83
471 487 1.890876 ATTAACAGGCGTGTCAGCAA 58.109 45.000 13.21 5.53 35.08 3.91
502 518 4.390048 GGGCTAGGCACGTTTGAA 57.610 55.556 19.14 0.00 0.00 2.69
543 559 2.481276 GGTCGTCATCATCGGTCAATGA 60.481 50.000 0.00 0.00 39.85 2.57
551 567 0.249120 ATCGGTCAATGACGCCTTGA 59.751 50.000 7.35 0.90 32.65 3.02
583 604 3.254014 GACGTGCAATTGTGGCGCT 62.254 57.895 7.64 1.41 39.53 5.92
593 614 3.484547 GTGGCGCTTTACGGTCCG 61.485 66.667 10.48 10.48 43.93 4.79
610 634 2.753966 CGGCGCAAATGAGGTCAGG 61.754 63.158 10.83 0.00 0.00 3.86
611 635 1.675641 GGCGCAAATGAGGTCAGGT 60.676 57.895 10.83 0.00 0.00 4.00
615 639 1.877680 CGCAAATGAGGTCAGGTGACA 60.878 52.381 12.09 0.00 46.47 3.58
623 647 5.304686 TGAGGTCAGGTGACAAAATAAGT 57.695 39.130 12.09 0.00 46.47 2.24
624 648 5.690865 TGAGGTCAGGTGACAAAATAAGTT 58.309 37.500 12.09 0.00 46.47 2.66
625 649 6.126409 TGAGGTCAGGTGACAAAATAAGTTT 58.874 36.000 12.09 0.00 46.47 2.66
645 669 0.250989 TTTTGAGGGGTTAGTGGGCG 60.251 55.000 0.00 0.00 0.00 6.13
654 678 2.356432 GGGTTAGTGGGCGAAATAAGGT 60.356 50.000 0.00 0.00 0.00 3.50
657 681 0.679960 AGTGGGCGAAATAAGGTGGC 60.680 55.000 0.00 0.00 0.00 5.01
664 688 0.335019 GAAATAAGGTGGCCCAGGGT 59.665 55.000 7.55 0.00 0.00 4.34
665 689 0.335019 AAATAAGGTGGCCCAGGGTC 59.665 55.000 1.68 1.68 0.00 4.46
666 690 0.552615 AATAAGGTGGCCCAGGGTCT 60.553 55.000 12.68 0.00 0.00 3.85
667 691 0.345502 ATAAGGTGGCCCAGGGTCTA 59.654 55.000 12.68 0.00 0.00 2.59
668 692 0.119561 TAAGGTGGCCCAGGGTCTAA 59.880 55.000 12.68 0.00 0.00 2.10
669 693 0.774491 AAGGTGGCCCAGGGTCTAAA 60.774 55.000 12.68 0.00 0.00 1.85
670 694 0.774491 AGGTGGCCCAGGGTCTAAAA 60.774 55.000 12.68 0.00 0.00 1.52
671 695 0.113580 GGTGGCCCAGGGTCTAAAAA 59.886 55.000 12.68 0.00 0.00 1.94
672 696 1.273041 GGTGGCCCAGGGTCTAAAAAT 60.273 52.381 12.68 0.00 0.00 1.82
673 697 2.536066 GTGGCCCAGGGTCTAAAAATT 58.464 47.619 12.68 0.00 0.00 1.82
674 698 3.564790 GGTGGCCCAGGGTCTAAAAATTA 60.565 47.826 12.68 0.00 0.00 1.40
675 699 4.286707 GTGGCCCAGGGTCTAAAAATTAT 58.713 43.478 12.68 0.00 0.00 1.28
676 700 5.451354 GTGGCCCAGGGTCTAAAAATTATA 58.549 41.667 12.68 0.00 0.00 0.98
677 701 5.301045 GTGGCCCAGGGTCTAAAAATTATAC 59.699 44.000 12.68 0.00 0.00 1.47
829 1365 7.752695 AGAAAACTCTCGCCAAATATAAACAG 58.247 34.615 0.00 0.00 0.00 3.16
938 1475 1.815421 CCCGCTGTTCCATTCGAGG 60.815 63.158 0.00 0.00 0.00 4.63
939 1476 1.815421 CCGCTGTTCCATTCGAGGG 60.815 63.158 0.00 0.00 0.00 4.30
964 1501 2.725203 TTTCCACCAACGCTCCCTCG 62.725 60.000 0.00 0.00 0.00 4.63
1398 1935 1.324740 CCGACCCCGTCAGGTATTCA 61.325 60.000 0.00 0.00 41.42 2.57
1432 1969 1.732941 ACGCAGCATCGTGGAAATTA 58.267 45.000 2.45 0.00 41.62 1.40
1496 2034 2.147315 TTTCTCTGCTGCTCGACGCT 62.147 55.000 0.00 0.00 40.11 5.07
1562 2100 6.710278 TGGAGATGATTTGATCTGTGTTACA 58.290 36.000 0.00 0.00 32.57 2.41
1567 2105 9.376075 AGATGATTTGATCTGTGTTACACTTAG 57.624 33.333 16.79 6.77 35.11 2.18
1596 2134 5.572511 GCGCAATTTGATTTGATCTGTGTTA 59.427 36.000 0.30 0.00 0.00 2.41
1617 2156 4.569761 AGTACCATCAGTAGTGCATACG 57.430 45.455 0.00 0.00 39.55 3.06
1735 2287 1.135402 GCACGTGATTTTGTGGGGATC 60.135 52.381 22.23 0.00 36.61 3.36
1820 2372 8.737168 AGCTAATGTTAAGATTTCTATGTGCA 57.263 30.769 2.84 0.00 0.00 4.57
1875 2427 1.122019 AGTGTTCAGGGCGGTCTCTT 61.122 55.000 0.00 0.00 0.00 2.85
1876 2428 0.250338 GTGTTCAGGGCGGTCTCTTT 60.250 55.000 0.00 0.00 0.00 2.52
1877 2429 0.250295 TGTTCAGGGCGGTCTCTTTG 60.250 55.000 0.00 0.00 0.00 2.77
1878 2430 0.250338 GTTCAGGGCGGTCTCTTTGT 60.250 55.000 0.00 0.00 0.00 2.83
1961 2513 1.064463 GGGAGGCATTTCTGGTGATGA 60.064 52.381 0.00 0.00 0.00 2.92
2322 2875 6.618287 TTGTTGTTGTCTCAGATAAACCTG 57.382 37.500 1.79 0.00 35.55 4.00
2323 2876 5.680619 TGTTGTTGTCTCAGATAAACCTGT 58.319 37.500 1.79 0.00 35.71 4.00
2361 2914 7.786178 AAAAAGGAAGACAAACTTTTATGGC 57.214 32.000 0.00 0.00 41.91 4.40
2531 3084 8.301002 AGCATATTCGATCTAGGAAAAGACTAC 58.699 37.037 0.00 0.00 0.00 2.73
2532 3085 8.082852 GCATATTCGATCTAGGAAAAGACTACA 58.917 37.037 0.00 0.00 0.00 2.74
2599 3152 9.189723 CTATTTCGTATAGTTTGGTACTTAGGC 57.810 37.037 0.00 0.00 38.33 3.93
2687 3240 6.586082 CCTCCGTTCCAAAATAATTGAAGTTG 59.414 38.462 0.00 0.00 0.00 3.16
2925 3479 1.577736 ACAGAGGGAGCAGCTTGTAT 58.422 50.000 0.00 0.00 0.00 2.29
2972 3610 6.867662 ATTTAGACATTATGCACTGCTACC 57.132 37.500 1.98 0.00 0.00 3.18
3108 4461 0.811616 GGGCCGAGTGCTACTTGATG 60.812 60.000 0.00 0.00 40.92 3.07
3112 4465 2.416836 GCCGAGTGCTACTTGATGTACA 60.417 50.000 0.00 0.00 36.87 2.90
3302 4655 1.139058 GTGTCCCGCAGTGGAAGATAT 59.861 52.381 0.00 0.00 42.00 1.63
3396 4749 3.473625 ACCGTAATATACTGGGCTTTGC 58.526 45.455 0.00 0.00 0.00 3.68
3744 5101 3.673746 TTATGACTGTTATGCTTGCGC 57.326 42.857 0.00 0.00 0.00 6.09
3780 5140 4.646572 GAACTGGTTTCCATTCTCAGTCT 58.353 43.478 0.00 0.00 37.66 3.24
3785 5145 4.257731 GGTTTCCATTCTCAGTCTTCCTC 58.742 47.826 0.00 0.00 0.00 3.71
3788 5148 3.796111 TCCATTCTCAGTCTTCCTCCTT 58.204 45.455 0.00 0.00 0.00 3.36
3789 5149 3.772025 TCCATTCTCAGTCTTCCTCCTTC 59.228 47.826 0.00 0.00 0.00 3.46
3798 5158 1.556911 TCTTCCTCCTTCTCATGCACC 59.443 52.381 0.00 0.00 0.00 5.01
3882 5242 1.534028 GCGCACATGGTTATGTTTCG 58.466 50.000 0.30 0.00 45.01 3.46
3885 5245 2.158645 CGCACATGGTTATGTTTCGTCA 59.841 45.455 0.00 0.00 45.01 4.35
3960 5320 4.750598 TGTCGAGATATGGAGTTCTAGTCG 59.249 45.833 0.00 0.00 0.00 4.18
4113 5473 3.658757 TTGTTTTGAAGGTATGCTGGC 57.341 42.857 0.00 0.00 0.00 4.85
4183 5544 9.675464 TTAAACCGTAAGATCATAACTGGAATT 57.325 29.630 0.00 0.00 43.02 2.17
4294 5655 1.123077 TGACCTCGCCAGCTATTCAT 58.877 50.000 0.00 0.00 0.00 2.57
4363 5728 6.598064 CCTTTATTTCTAGTGGTTACTGTGGG 59.402 42.308 0.00 0.00 37.78 4.61
4367 5732 5.376756 TTCTAGTGGTTACTGTGGGTTTT 57.623 39.130 0.00 0.00 37.78 2.43
4520 5889 7.516198 TGGAACGAGATTAGTAGGGTAATAC 57.484 40.000 0.00 0.00 0.00 1.89
4530 5899 9.406113 GATTAGTAGGGTAATACCTATCGACAT 57.594 37.037 9.58 0.00 44.48 3.06
4558 5927 6.350194 GGGAGATTTAGGTCCACATTTCAAAC 60.350 42.308 0.00 0.00 34.14 2.93
4618 5988 4.415596 TGTGCTAAAATCCATTGTCCCTT 58.584 39.130 0.00 0.00 0.00 3.95
4761 6296 5.741011 TGGACATATACAAAAGGACAGACC 58.259 41.667 0.00 0.00 39.35 3.85
4762 6297 5.123936 GGACATATACAAAAGGACAGACCC 58.876 45.833 0.00 0.00 40.05 4.46
4763 6298 5.338871 GGACATATACAAAAGGACAGACCCA 60.339 44.000 0.00 0.00 40.05 4.51
4764 6299 5.745227 ACATATACAAAAGGACAGACCCAG 58.255 41.667 0.00 0.00 40.05 4.45
4765 6300 5.250774 ACATATACAAAAGGACAGACCCAGT 59.749 40.000 0.00 0.00 40.05 4.00
4766 6301 2.348411 ACAAAAGGACAGACCCAGTG 57.652 50.000 0.00 0.00 40.05 3.66
4767 6302 0.954452 CAAAAGGACAGACCCAGTGC 59.046 55.000 0.00 0.00 40.05 4.40
4768 6303 0.550914 AAAAGGACAGACCCAGTGCA 59.449 50.000 0.00 0.00 40.05 4.57
4769 6304 0.179018 AAAGGACAGACCCAGTGCAC 60.179 55.000 9.40 9.40 40.05 4.57
4770 6305 1.056700 AAGGACAGACCCAGTGCACT 61.057 55.000 15.25 15.25 40.05 4.40
4771 6306 1.056700 AGGACAGACCCAGTGCACTT 61.057 55.000 18.94 2.02 40.05 3.16
4772 6307 0.603975 GGACAGACCCAGTGCACTTC 60.604 60.000 18.94 13.01 0.00 3.01
4773 6308 0.394565 GACAGACCCAGTGCACTTCT 59.605 55.000 18.94 15.33 0.00 2.85
4774 6309 0.394565 ACAGACCCAGTGCACTTCTC 59.605 55.000 18.94 11.63 0.00 2.87
4775 6310 0.668706 CAGACCCAGTGCACTTCTCG 60.669 60.000 18.94 5.70 0.00 4.04
4776 6311 1.374758 GACCCAGTGCACTTCTCGG 60.375 63.158 18.94 15.35 0.00 4.63
4777 6312 2.100879 GACCCAGTGCACTTCTCGGT 62.101 60.000 18.94 19.29 0.00 4.69
4778 6313 1.669115 CCCAGTGCACTTCTCGGTG 60.669 63.158 18.94 4.67 39.91 4.94
4779 6314 1.069765 CCAGTGCACTTCTCGGTGT 59.930 57.895 18.94 0.00 39.21 4.16
4780 6315 0.946221 CCAGTGCACTTCTCGGTGTC 60.946 60.000 18.94 0.00 39.21 3.67
4781 6316 0.032678 CAGTGCACTTCTCGGTGTCT 59.967 55.000 18.94 0.00 39.21 3.41
4782 6317 0.032678 AGTGCACTTCTCGGTGTCTG 59.967 55.000 15.25 0.00 39.21 3.51
4783 6318 0.946221 GTGCACTTCTCGGTGTCTGG 60.946 60.000 10.32 0.00 39.21 3.86
4784 6319 1.374758 GCACTTCTCGGTGTCTGGG 60.375 63.158 0.00 0.00 39.21 4.45
4785 6320 1.293498 CACTTCTCGGTGTCTGGGG 59.707 63.158 0.00 0.00 33.04 4.96
4786 6321 1.155390 ACTTCTCGGTGTCTGGGGA 59.845 57.895 0.00 0.00 0.00 4.81
4787 6322 0.900647 ACTTCTCGGTGTCTGGGGAG 60.901 60.000 0.00 0.00 0.00 4.30
4788 6323 1.608717 CTTCTCGGTGTCTGGGGAGG 61.609 65.000 0.00 0.00 0.00 4.30
4789 6324 3.077556 CTCGGTGTCTGGGGAGGG 61.078 72.222 0.00 0.00 0.00 4.30
4790 6325 3.596799 TCGGTGTCTGGGGAGGGA 61.597 66.667 0.00 0.00 0.00 4.20
4791 6326 2.365635 CGGTGTCTGGGGAGGGAT 60.366 66.667 0.00 0.00 0.00 3.85
4792 6327 1.995626 CGGTGTCTGGGGAGGGATT 60.996 63.158 0.00 0.00 0.00 3.01
4793 6328 0.689745 CGGTGTCTGGGGAGGGATTA 60.690 60.000 0.00 0.00 0.00 1.75
4794 6329 1.821088 GGTGTCTGGGGAGGGATTAT 58.179 55.000 0.00 0.00 0.00 1.28
4795 6330 2.758640 CGGTGTCTGGGGAGGGATTATA 60.759 54.545 0.00 0.00 0.00 0.98
4796 6331 2.907042 GGTGTCTGGGGAGGGATTATAG 59.093 54.545 0.00 0.00 0.00 1.31
4797 6332 3.439558 GGTGTCTGGGGAGGGATTATAGA 60.440 52.174 0.00 0.00 0.00 1.98
4798 6333 4.232091 GTGTCTGGGGAGGGATTATAGAA 58.768 47.826 0.00 0.00 0.00 2.10
4799 6334 4.040584 GTGTCTGGGGAGGGATTATAGAAC 59.959 50.000 0.00 0.00 0.00 3.01
4800 6335 3.583526 GTCTGGGGAGGGATTATAGAACC 59.416 52.174 0.00 0.00 0.00 3.62
4801 6336 3.475174 TCTGGGGAGGGATTATAGAACCT 59.525 47.826 0.00 0.00 35.67 3.50
4802 6337 4.677983 TCTGGGGAGGGATTATAGAACCTA 59.322 45.833 0.00 0.00 32.42 3.08
4803 6338 4.759953 TGGGGAGGGATTATAGAACCTAC 58.240 47.826 0.00 0.00 32.42 3.18
4804 6339 4.426023 TGGGGAGGGATTATAGAACCTACT 59.574 45.833 0.00 0.00 34.26 2.57
4805 6340 5.024785 GGGGAGGGATTATAGAACCTACTC 58.975 50.000 0.00 0.00 34.26 2.59
4806 6341 5.222589 GGGGAGGGATTATAGAACCTACTCT 60.223 48.000 0.00 0.00 31.34 3.24
4807 6342 6.324544 GGGAGGGATTATAGAACCTACTCTT 58.675 44.000 0.00 0.00 34.26 2.85
4808 6343 7.477008 GGGAGGGATTATAGAACCTACTCTTA 58.523 42.308 0.00 0.00 34.26 2.10
4809 6344 7.396907 GGGAGGGATTATAGAACCTACTCTTAC 59.603 44.444 0.00 0.00 34.26 2.34
4810 6345 7.396907 GGAGGGATTATAGAACCTACTCTTACC 59.603 44.444 0.00 0.00 32.42 2.85
4811 6346 7.247500 AGGGATTATAGAACCTACTCTTACCC 58.753 42.308 0.00 0.00 0.00 3.69
4812 6347 6.440010 GGGATTATAGAACCTACTCTTACCCC 59.560 46.154 0.00 0.00 0.00 4.95
4813 6348 7.247500 GGATTATAGAACCTACTCTTACCCCT 58.753 42.308 0.00 0.00 0.00 4.79
4814 6349 7.178805 GGATTATAGAACCTACTCTTACCCCTG 59.821 44.444 0.00 0.00 0.00 4.45
4815 6350 2.468915 AGAACCTACTCTTACCCCTGC 58.531 52.381 0.00 0.00 0.00 4.85
4816 6351 2.185387 GAACCTACTCTTACCCCTGCA 58.815 52.381 0.00 0.00 0.00 4.41
4817 6352 2.337359 ACCTACTCTTACCCCTGCAA 57.663 50.000 0.00 0.00 0.00 4.08
4818 6353 2.627933 ACCTACTCTTACCCCTGCAAA 58.372 47.619 0.00 0.00 0.00 3.68
4819 6354 2.572104 ACCTACTCTTACCCCTGCAAAG 59.428 50.000 0.00 0.00 0.00 2.77
4820 6355 2.572104 CCTACTCTTACCCCTGCAAAGT 59.428 50.000 0.00 0.00 0.00 2.66
4821 6356 2.568623 ACTCTTACCCCTGCAAAGTG 57.431 50.000 0.00 0.00 0.00 3.16
4822 6357 1.168714 CTCTTACCCCTGCAAAGTGC 58.831 55.000 0.00 0.00 45.29 4.40
4833 6368 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
4834 6369 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
4835 6370 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
4836 6371 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
4838 6373 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
4839 6374 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
4840 6375 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
4841 6376 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
4842 6377 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.000 0.00 0.00 45.03 3.95
4843 6378 1.260538 ATGCAGAGAGGCTGGTTCGA 61.261 55.000 0.00 0.00 45.03 3.71
4844 6379 1.293498 GCAGAGAGGCTGGTTCGAA 59.707 57.895 0.00 0.00 45.03 3.71
4845 6380 1.016653 GCAGAGAGGCTGGTTCGAAC 61.017 60.000 20.14 20.14 45.03 3.95
4854 6389 3.479979 GGTTCGAACCCAGGACCT 58.520 61.111 33.02 0.00 43.43 3.85
4855 6390 1.295746 GGTTCGAACCCAGGACCTC 59.704 63.158 33.02 7.79 43.43 3.85
4856 6391 1.192803 GGTTCGAACCCAGGACCTCT 61.193 60.000 33.02 0.00 43.43 3.69
4857 6392 0.685660 GTTCGAACCCAGGACCTCTT 59.314 55.000 17.68 0.00 0.00 2.85
4858 6393 0.685097 TTCGAACCCAGGACCTCTTG 59.315 55.000 0.00 0.00 0.00 3.02
4859 6394 1.192146 TCGAACCCAGGACCTCTTGG 61.192 60.000 0.00 0.00 42.20 3.61
4860 6395 1.002011 GAACCCAGGACCTCTTGGC 60.002 63.158 0.00 0.00 41.31 4.52
4861 6396 1.774217 AACCCAGGACCTCTTGGCA 60.774 57.895 0.00 0.00 41.31 4.92
4862 6397 2.069165 AACCCAGGACCTCTTGGCAC 62.069 60.000 0.00 0.00 41.31 5.01
4863 6398 2.528818 CCCAGGACCTCTTGGCACA 61.529 63.158 0.00 0.00 41.31 4.57
4874 6409 2.449518 TGGCACAAGTGGGGAGGA 60.450 61.111 2.00 0.00 31.92 3.71
4875 6410 2.034221 GGCACAAGTGGGGAGGAC 59.966 66.667 2.00 0.00 0.00 3.85
4876 6411 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
4877 6412 1.456287 GCACAAGTGGGGAGGACTT 59.544 57.895 2.00 0.00 33.82 3.01
4878 6413 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.000 2.00 0.00 31.05 3.01
4879 6414 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.000 0.00 0.00 31.05 3.02
4880 6415 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.000 0.00 0.00 31.05 3.18
4886 6421 1.003233 GGGAGGACTTCACCACTGC 60.003 63.158 0.00 0.00 0.00 4.40
4887 6422 1.374758 GGAGGACTTCACCACTGCG 60.375 63.158 0.00 0.00 0.00 5.18
4888 6423 2.029844 GAGGACTTCACCACTGCGC 61.030 63.158 0.00 0.00 0.00 6.09
4889 6424 3.050275 GGACTTCACCACTGCGCC 61.050 66.667 4.18 0.00 0.00 6.53
4890 6425 2.280797 GACTTCACCACTGCGCCA 60.281 61.111 4.18 0.00 0.00 5.69
4891 6426 2.281070 ACTTCACCACTGCGCCAG 60.281 61.111 4.18 4.99 37.52 4.85
4892 6427 3.052082 CTTCACCACTGCGCCAGG 61.052 66.667 4.18 6.64 35.51 4.45
4904 6439 3.411517 GCCAGGCCTGCCCTCTTA 61.412 66.667 28.39 0.00 44.09 2.10
4905 6440 2.761465 GCCAGGCCTGCCCTCTTAT 61.761 63.158 28.39 0.00 44.09 1.73
4906 6441 1.418908 GCCAGGCCTGCCCTCTTATA 61.419 60.000 28.39 0.00 44.09 0.98
4907 6442 1.366319 CCAGGCCTGCCCTCTTATAT 58.634 55.000 28.39 0.00 44.09 0.86
4908 6443 1.004044 CCAGGCCTGCCCTCTTATATG 59.996 57.143 28.39 4.96 44.09 1.78
4909 6444 1.004044 CAGGCCTGCCCTCTTATATGG 59.996 57.143 22.33 0.00 44.09 2.74
4910 6445 1.132397 AGGCCTGCCCTCTTATATGGA 60.132 52.381 3.11 0.00 41.21 3.41
4911 6446 1.003696 GGCCTGCCCTCTTATATGGAC 59.996 57.143 0.00 0.00 0.00 4.02
4912 6447 1.699634 GCCTGCCCTCTTATATGGACA 59.300 52.381 0.00 0.00 0.00 4.02
4913 6448 2.307098 GCCTGCCCTCTTATATGGACAT 59.693 50.000 0.00 0.00 0.00 3.06
4914 6449 3.519510 GCCTGCCCTCTTATATGGACATA 59.480 47.826 0.00 0.00 0.00 2.29
4915 6450 4.164988 GCCTGCCCTCTTATATGGACATAT 59.835 45.833 9.53 9.53 37.69 1.78
5022 6743 6.862608 TGCAATATAGCTTGTTGTGAAGTTTG 59.137 34.615 0.00 0.00 34.99 2.93
5041 6762 7.264373 AGTTTGAACTTCAGTATTCCACAAG 57.736 36.000 0.00 0.00 35.21 3.16
5042 6763 7.054124 AGTTTGAACTTCAGTATTCCACAAGA 58.946 34.615 0.00 0.00 35.21 3.02
5043 6764 7.227512 AGTTTGAACTTCAGTATTCCACAAGAG 59.772 37.037 0.00 0.00 35.21 2.85
5092 6818 7.095691 CCGAGTGTTGCATTTTTGTTATGAAAT 60.096 33.333 0.00 0.00 0.00 2.17
5134 6860 9.030301 CAGTAATTTTGATTTGTTCTTTCCGTT 57.970 29.630 0.00 0.00 0.00 4.44
5400 7128 4.625028 TGAAGATCAAGTATGCAGATCCG 58.375 43.478 8.77 0.00 39.10 4.18
5482 7210 7.891183 TCATACTTGCAGAGAAACTTAAGTC 57.109 36.000 8.95 0.00 36.00 3.01
5559 7287 3.914426 AGAGCATCCCAACGACTTTAT 57.086 42.857 0.00 0.00 33.66 1.40
5628 7356 7.926555 GGATATTTACATGACCTTCTCTTCGAA 59.073 37.037 0.00 0.00 0.00 3.71
5803 7531 2.432146 TCTGCCGCTGTCTTCATAGATT 59.568 45.455 0.00 0.00 31.86 2.40
5945 7674 7.230849 AGTTCAATATTTGTTGCTGGATTGA 57.769 32.000 0.00 0.00 32.86 2.57
6071 7807 1.807139 ATGTTACTGATGTGCGCACA 58.193 45.000 41.97 41.97 46.44 4.57
6089 7825 4.271776 CGCACAAGCAGATTAATGATGAGA 59.728 41.667 0.00 0.00 42.27 3.27
6128 7864 4.269603 GCAGTGTCAGCTATGTTATCACAG 59.730 45.833 0.00 0.00 35.94 3.66
6190 7926 4.031611 AGTCCAACCCCTATTACAGTCTC 58.968 47.826 0.00 0.00 0.00 3.36
6206 7942 2.490903 AGTCTCGTGTGGCGTAAGTTAT 59.509 45.455 0.00 0.00 42.13 1.89
6215 7951 5.050567 GTGTGGCGTAAGTTATAATGGTAGC 60.051 44.000 0.00 0.00 41.68 3.58
6368 8104 4.103153 TCCCTTTGTTGAGTCAGACTTCAT 59.897 41.667 4.05 0.00 0.00 2.57
6551 8287 6.459670 TCTGAAATGAAATGATGATGTGGG 57.540 37.500 0.00 0.00 0.00 4.61
6580 8317 9.927081 AGATTACATTGGAGGATCATAGTTTTT 57.073 29.630 0.00 0.00 36.25 1.94
6821 8559 5.132897 ACTTTCTTTTTGTGTCAACTGCA 57.867 34.783 0.00 0.00 0.00 4.41
6859 8597 4.021016 CCATCCTTCTGTACCAGCTATACC 60.021 50.000 5.16 0.00 0.00 2.73
7116 8854 7.066374 TCGTTTCCTTTGAAATTTTGGTTTG 57.934 32.000 0.00 0.00 42.20 2.93
7609 9373 7.151308 TGCACCAGTTATTTTCTTTACCAATG 58.849 34.615 0.00 0.00 0.00 2.82
7618 9382 9.651913 TTATTTTCTTTACCAATGGAGATTTGC 57.348 29.630 6.16 0.00 0.00 3.68
7669 9433 2.550830 TCCCTCTGTGCTGAAGTTTC 57.449 50.000 0.00 0.00 0.00 2.78
7727 9491 5.047872 TGCATGCAGTGAATTAACAGTTCAT 60.048 36.000 18.46 0.00 37.84 2.57
7742 9506 5.097529 ACAGTTCATAAAATGCTGCAATCG 58.902 37.500 6.36 0.00 33.83 3.34
7909 9673 7.114754 TGAACAATCAGATATCTCCTTTGCTT 58.885 34.615 1.03 4.86 0.00 3.91
7974 9741 4.927978 ACCATCGTCATAAGAGAGAAGG 57.072 45.455 0.00 0.00 31.03 3.46
7996 9763 3.855154 GCACCATGTATCTAGCTCAGACG 60.855 52.174 0.00 0.00 35.62 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.142381 CGATATCACTGTGTCAGAGGTGAA 60.142 45.833 7.79 0.00 41.14 3.18
47 48 1.227263 GGGTGCGCACGATATCACT 60.227 57.895 32.35 0.00 0.00 3.41
74 75 1.893315 CCCTCCCATTCCTTCTACCA 58.107 55.000 0.00 0.00 0.00 3.25
89 90 3.011517 TCCTCCTGCTTGGCCCTC 61.012 66.667 0.00 0.00 35.26 4.30
90 91 3.013932 CTCCTCCTGCTTGGCCCT 61.014 66.667 0.00 0.00 35.26 5.19
94 95 3.333219 TGCCCTCCTCCTGCTTGG 61.333 66.667 0.00 0.00 37.10 3.61
110 114 3.201290 CTCCATCTTCATCCTTTCCGTG 58.799 50.000 0.00 0.00 0.00 4.94
111 115 2.171448 CCTCCATCTTCATCCTTTCCGT 59.829 50.000 0.00 0.00 0.00 4.69
177 181 4.284746 ACTGGGGATTTAGATCGATCTTCC 59.715 45.833 31.55 28.64 38.32 3.46
236 251 1.640428 TTGATCTTTAGACGCGGCAG 58.360 50.000 17.71 2.05 0.00 4.85
244 259 6.704493 ACTGTTGCGTTACTTTGATCTTTAGA 59.296 34.615 0.00 0.00 0.00 2.10
265 280 9.030452 TGCCAGGTAAAATTAAAATATGACTGT 57.970 29.630 0.00 0.00 0.00 3.55
267 282 9.255029 ACTGCCAGGTAAAATTAAAATATGACT 57.745 29.630 0.00 0.00 0.00 3.41
270 285 9.868277 TTGACTGCCAGGTAAAATTAAAATATG 57.132 29.630 0.00 0.00 0.00 1.78
306 321 2.059190 TGTTATACCGCCTGCCCGA 61.059 57.895 0.00 0.00 0.00 5.14
328 343 0.464036 CCTAGGCATCAGGCGTGTTA 59.536 55.000 6.26 0.00 46.16 2.41
356 371 5.363292 TGGTTAGGCGTGTATCTTACCATAA 59.637 40.000 0.00 0.00 37.65 1.90
393 408 1.959985 TGGTGTGCACTTGTTAATGGG 59.040 47.619 19.41 0.00 0.00 4.00
431 446 0.791422 CGGCGTTTAACCACAATCGA 59.209 50.000 0.00 0.00 0.00 3.59
494 510 2.542907 CGTGGCAGCCTTCAAACGT 61.543 57.895 14.15 0.00 0.00 3.99
529 545 0.465705 AGGCGTCATTGACCGATGAT 59.534 50.000 11.12 0.00 38.25 2.45
561 582 2.636462 CACAATTGCACGTCGCCA 59.364 55.556 5.05 0.00 41.33 5.69
574 595 1.962306 GGACCGTAAAGCGCCACAA 60.962 57.895 2.29 0.00 39.71 3.33
583 604 1.671704 ATTTGCGCCGGACCGTAAA 60.672 52.632 16.99 16.99 44.42 2.01
593 614 1.675641 ACCTGACCTCATTTGCGCC 60.676 57.895 4.18 0.00 0.00 6.53
598 619 6.777580 ACTTATTTTGTCACCTGACCTCATTT 59.222 34.615 2.98 0.00 44.15 2.32
625 649 1.820090 CGCCCACTAACCCCTCAAAAA 60.820 52.381 0.00 0.00 0.00 1.94
631 655 1.587066 TATTTCGCCCACTAACCCCT 58.413 50.000 0.00 0.00 0.00 4.79
637 661 1.407712 GCCACCTTATTTCGCCCACTA 60.408 52.381 0.00 0.00 0.00 2.74
645 669 0.335019 ACCCTGGGCCACCTTATTTC 59.665 55.000 14.08 0.00 37.76 2.17
654 678 4.618378 ATAATTTTTAGACCCTGGGCCA 57.382 40.909 14.08 5.85 0.00 5.36
664 688 8.810990 ATGTTGAACGGGGTATAATTTTTAGA 57.189 30.769 0.00 0.00 0.00 2.10
665 689 8.899771 AGATGTTGAACGGGGTATAATTTTTAG 58.100 33.333 0.00 0.00 0.00 1.85
666 690 8.810990 AGATGTTGAACGGGGTATAATTTTTA 57.189 30.769 0.00 0.00 0.00 1.52
667 691 7.414762 CGAGATGTTGAACGGGGTATAATTTTT 60.415 37.037 0.00 0.00 0.00 1.94
668 692 6.037830 CGAGATGTTGAACGGGGTATAATTTT 59.962 38.462 0.00 0.00 0.00 1.82
669 693 5.526111 CGAGATGTTGAACGGGGTATAATTT 59.474 40.000 0.00 0.00 0.00 1.82
670 694 5.054477 CGAGATGTTGAACGGGGTATAATT 58.946 41.667 0.00 0.00 0.00 1.40
671 695 4.100498 ACGAGATGTTGAACGGGGTATAAT 59.900 41.667 0.00 0.00 0.00 1.28
672 696 3.448301 ACGAGATGTTGAACGGGGTATAA 59.552 43.478 0.00 0.00 0.00 0.98
673 697 3.025978 ACGAGATGTTGAACGGGGTATA 58.974 45.455 0.00 0.00 0.00 1.47
674 698 1.829222 ACGAGATGTTGAACGGGGTAT 59.171 47.619 0.00 0.00 0.00 2.73
675 699 1.203052 GACGAGATGTTGAACGGGGTA 59.797 52.381 0.00 0.00 0.00 3.69
676 700 0.037605 GACGAGATGTTGAACGGGGT 60.038 55.000 0.00 0.00 0.00 4.95
677 701 0.739813 GGACGAGATGTTGAACGGGG 60.740 60.000 0.00 0.00 0.00 5.73
794 1330 3.537613 GCGAGAGTTTTCTAACGTAGACG 59.462 47.826 0.00 0.00 39.31 4.18
829 1365 1.140804 GGTCTCTCCTTGAGCTCGC 59.859 63.158 9.64 0.00 42.38 5.03
857 1394 1.318785 CGCGAGAAATCTGTCGTCAAG 59.681 52.381 0.00 0.00 40.35 3.02
964 1501 4.131088 GTGGGTCGCTCCGAGGAC 62.131 72.222 0.00 3.36 36.23 3.85
1147 1684 2.460275 CCATTTCCGATGCACGCGA 61.460 57.895 15.93 0.00 41.07 5.87
1218 1755 4.593864 GCGTCCATCTCCTCCGCC 62.594 72.222 0.00 0.00 38.52 6.13
1398 1935 1.659794 GCGTTGGCAAATGAGGTGT 59.340 52.632 0.00 0.00 39.62 4.16
1432 1969 6.101332 TCGGTGCTACTACGATAACAAATTT 58.899 36.000 0.00 0.00 0.00 1.82
1496 2034 2.590291 ACGCGTGATGCCACAACA 60.590 55.556 12.93 0.00 43.34 3.33
1530 2068 8.420222 ACAGATCAAATCATCTCCAACTACTAG 58.580 37.037 0.00 0.00 30.07 2.57
1562 2100 4.519540 ATCAAATTGCGCCAAACTAAGT 57.480 36.364 4.18 0.00 0.00 2.24
1567 2105 4.389687 AGATCAAATCAAATTGCGCCAAAC 59.610 37.500 4.18 0.00 0.00 2.93
1596 2134 3.243434 GCGTATGCACTACTGATGGTACT 60.243 47.826 0.89 0.00 42.15 2.73
1820 2372 3.978610 AGTCCCTTGTAATCTAGTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
2361 2914 6.039382 AGGTTGCTAACTCCACTTTTAAGTTG 59.961 38.462 0.00 0.00 37.08 3.16
2531 3084 2.261345 CGCCAAGTGCAAACCATAATG 58.739 47.619 0.00 0.00 41.33 1.90
2532 3085 1.204467 CCGCCAAGTGCAAACCATAAT 59.796 47.619 0.00 0.00 41.33 1.28
2599 3152 4.682778 TTAATGTATCCCGAGTTCCCTG 57.317 45.455 0.00 0.00 0.00 4.45
2687 3240 9.726232 AAAAAGTTTGACTTACGAAAATCCTAC 57.274 29.630 0.00 0.00 37.47 3.18
2729 3282 8.926710 CGTAGATCTTTGCGGATTTTTCTATAT 58.073 33.333 0.00 0.00 0.00 0.86
2943 3497 8.727910 AGCAGTGCATAATGTCTAAATATGATG 58.272 33.333 19.20 0.00 30.32 3.07
3067 4420 6.591834 GCCCATATGATGATACAGTAACAGTC 59.408 42.308 3.65 0.00 0.00 3.51
3247 4600 5.025453 AGCAAAACCCACTATGGAAATCAT 58.975 37.500 0.00 0.00 40.96 2.45
3255 4608 2.095059 GCTGTCAGCAAAACCCACTATG 60.095 50.000 20.16 0.00 41.89 2.23
3302 4655 4.825422 TCAACAACTTTGCAAAATGGTCA 58.175 34.783 21.84 6.01 0.00 4.02
3741 5098 3.423154 CGTTCACTTCCAGGGCGC 61.423 66.667 0.00 0.00 0.00 6.53
3744 5101 1.512926 CAGTTCGTTCACTTCCAGGG 58.487 55.000 0.00 0.00 0.00 4.45
3780 5140 1.280133 CAGGTGCATGAGAAGGAGGAA 59.720 52.381 0.00 0.00 0.00 3.36
3785 5145 0.617413 ACTCCAGGTGCATGAGAAGG 59.383 55.000 0.00 0.00 0.00 3.46
3788 5148 1.649321 AAGACTCCAGGTGCATGAGA 58.351 50.000 0.00 0.00 0.00 3.27
3789 5149 2.027377 AGAAAGACTCCAGGTGCATGAG 60.027 50.000 0.00 0.00 0.00 2.90
3798 5158 9.346725 GCAACAATTTAATAAGAAAGACTCCAG 57.653 33.333 0.00 0.00 0.00 3.86
3827 5187 3.717707 TGTCCTTGAGAGAAAAGACACG 58.282 45.455 0.00 0.00 0.00 4.49
3882 5242 2.816087 ACCAACAGCATGATCAAGTGAC 59.184 45.455 0.00 0.00 39.69 3.67
3885 5245 2.816087 GTCACCAACAGCATGATCAAGT 59.184 45.455 0.00 0.00 39.69 3.16
3960 5320 6.944234 AAGCCCAGATACAAAATAAGCTAC 57.056 37.500 0.00 0.00 0.00 3.58
4199 5560 8.533657 TGAATGATCAGCAAACAAAAGGAATAT 58.466 29.630 0.09 0.00 0.00 1.28
4294 5655 1.194218 TCGGATGAGATGGCTGAACA 58.806 50.000 0.00 0.00 0.00 3.18
4333 5698 7.552687 CAGTAACCACTAGAAATAAAGGCATCA 59.447 37.037 0.00 0.00 32.21 3.07
4343 5708 5.578157 AACCCACAGTAACCACTAGAAAT 57.422 39.130 0.00 0.00 32.21 2.17
4367 5732 4.142049 CCACAGCAACCTTTGGTTAAGAAA 60.142 41.667 1.34 0.00 45.01 2.52
4370 5735 2.035832 CCCACAGCAACCTTTGGTTAAG 59.964 50.000 1.34 0.00 45.01 1.85
4377 5744 1.457455 CCACCCCACAGCAACCTTT 60.457 57.895 0.00 0.00 0.00 3.11
4520 5889 1.840737 ATCTCCCCGATGTCGATAGG 58.159 55.000 3.62 2.25 43.02 2.57
4530 5899 1.273381 TGTGGACCTAAATCTCCCCGA 60.273 52.381 0.00 0.00 0.00 5.14
4558 5927 8.950403 TTCTACGTATTGACATGATAAGATCG 57.050 34.615 0.00 3.67 0.00 3.69
4594 5963 4.016444 GGGACAATGGATTTTAGCACAGA 58.984 43.478 0.00 0.00 0.00 3.41
4618 5988 6.405731 GGAAGCATATCACAATGGCAAGTAAA 60.406 38.462 0.00 0.00 0.00 2.01
4748 6283 0.954452 GCACTGGGTCTGTCCTTTTG 59.046 55.000 0.00 0.00 36.25 2.44
4750 6285 0.179018 GTGCACTGGGTCTGTCCTTT 60.179 55.000 10.32 0.00 36.25 3.11
4751 6286 1.056700 AGTGCACTGGGTCTGTCCTT 61.057 55.000 20.97 0.00 36.25 3.36
4752 6287 1.056700 AAGTGCACTGGGTCTGTCCT 61.057 55.000 22.49 0.00 36.25 3.85
4753 6288 0.603975 GAAGTGCACTGGGTCTGTCC 60.604 60.000 22.49 0.00 0.00 4.02
4754 6289 0.394565 AGAAGTGCACTGGGTCTGTC 59.605 55.000 22.49 12.29 0.00 3.51
4755 6290 0.394565 GAGAAGTGCACTGGGTCTGT 59.605 55.000 22.49 1.76 0.00 3.41
4756 6291 0.668706 CGAGAAGTGCACTGGGTCTG 60.669 60.000 22.49 10.40 0.00 3.51
4757 6292 1.668294 CGAGAAGTGCACTGGGTCT 59.332 57.895 22.49 19.57 0.00 3.85
4758 6293 1.374758 CCGAGAAGTGCACTGGGTC 60.375 63.158 22.49 14.67 0.00 4.46
4759 6294 2.140792 ACCGAGAAGTGCACTGGGT 61.141 57.895 22.49 21.11 40.60 4.51
4760 6295 1.669115 CACCGAGAAGTGCACTGGG 60.669 63.158 22.49 20.46 38.79 4.45
4761 6296 0.946221 GACACCGAGAAGTGCACTGG 60.946 60.000 22.49 19.35 41.67 4.00
4762 6297 0.032678 AGACACCGAGAAGTGCACTG 59.967 55.000 22.49 10.04 41.67 3.66
4763 6298 0.032678 CAGACACCGAGAAGTGCACT 59.967 55.000 15.25 15.25 41.67 4.40
4764 6299 0.946221 CCAGACACCGAGAAGTGCAC 60.946 60.000 9.40 9.40 41.67 4.57
4765 6300 1.367471 CCAGACACCGAGAAGTGCA 59.633 57.895 0.00 0.00 41.67 4.57
4766 6301 1.374758 CCCAGACACCGAGAAGTGC 60.375 63.158 0.00 0.00 41.67 4.40
4767 6302 1.185618 TCCCCAGACACCGAGAAGTG 61.186 60.000 0.00 0.00 43.65 3.16
4768 6303 0.900647 CTCCCCAGACACCGAGAAGT 60.901 60.000 0.00 0.00 0.00 3.01
4769 6304 1.608717 CCTCCCCAGACACCGAGAAG 61.609 65.000 0.00 0.00 0.00 2.85
4770 6305 1.609501 CCTCCCCAGACACCGAGAA 60.610 63.158 0.00 0.00 0.00 2.87
4771 6306 2.037367 CCTCCCCAGACACCGAGA 59.963 66.667 0.00 0.00 0.00 4.04
4772 6307 2.880629 ATCCCTCCCCAGACACCGAG 62.881 65.000 0.00 0.00 0.00 4.63
4773 6308 2.471084 AATCCCTCCCCAGACACCGA 62.471 60.000 0.00 0.00 0.00 4.69
4774 6309 0.689745 TAATCCCTCCCCAGACACCG 60.690 60.000 0.00 0.00 0.00 4.94
4775 6310 1.821088 ATAATCCCTCCCCAGACACC 58.179 55.000 0.00 0.00 0.00 4.16
4776 6311 3.858135 TCTATAATCCCTCCCCAGACAC 58.142 50.000 0.00 0.00 0.00 3.67
4777 6312 4.232091 GTTCTATAATCCCTCCCCAGACA 58.768 47.826 0.00 0.00 0.00 3.41
4778 6313 3.583526 GGTTCTATAATCCCTCCCCAGAC 59.416 52.174 0.00 0.00 0.00 3.51
4779 6314 3.475174 AGGTTCTATAATCCCTCCCCAGA 59.525 47.826 0.00 0.00 0.00 3.86
4780 6315 3.875571 AGGTTCTATAATCCCTCCCCAG 58.124 50.000 0.00 0.00 0.00 4.45
4781 6316 4.426023 AGTAGGTTCTATAATCCCTCCCCA 59.574 45.833 0.00 0.00 0.00 4.96
4782 6317 5.024785 GAGTAGGTTCTATAATCCCTCCCC 58.975 50.000 0.00 0.00 0.00 4.81
4783 6318 5.906254 AGAGTAGGTTCTATAATCCCTCCC 58.094 45.833 0.00 0.00 0.00 4.30
4784 6319 7.396907 GGTAAGAGTAGGTTCTATAATCCCTCC 59.603 44.444 0.00 0.00 0.00 4.30
4785 6320 7.396907 GGGTAAGAGTAGGTTCTATAATCCCTC 59.603 44.444 0.00 0.00 0.00 4.30
4786 6321 7.247500 GGGTAAGAGTAGGTTCTATAATCCCT 58.753 42.308 0.00 0.00 0.00 4.20
4787 6322 6.440010 GGGGTAAGAGTAGGTTCTATAATCCC 59.560 46.154 0.00 0.00 0.00 3.85
4788 6323 7.178805 CAGGGGTAAGAGTAGGTTCTATAATCC 59.821 44.444 0.00 0.00 0.00 3.01
4789 6324 7.309928 GCAGGGGTAAGAGTAGGTTCTATAATC 60.310 44.444 0.00 0.00 0.00 1.75
4790 6325 6.497606 GCAGGGGTAAGAGTAGGTTCTATAAT 59.502 42.308 0.00 0.00 0.00 1.28
4791 6326 5.837438 GCAGGGGTAAGAGTAGGTTCTATAA 59.163 44.000 0.00 0.00 0.00 0.98
4792 6327 5.103387 TGCAGGGGTAAGAGTAGGTTCTATA 60.103 44.000 0.00 0.00 0.00 1.31
4793 6328 4.224762 GCAGGGGTAAGAGTAGGTTCTAT 58.775 47.826 0.00 0.00 0.00 1.98
4794 6329 3.012047 TGCAGGGGTAAGAGTAGGTTCTA 59.988 47.826 0.00 0.00 0.00 2.10
4795 6330 2.225547 TGCAGGGGTAAGAGTAGGTTCT 60.226 50.000 0.00 0.00 0.00 3.01
4796 6331 2.185387 TGCAGGGGTAAGAGTAGGTTC 58.815 52.381 0.00 0.00 0.00 3.62
4797 6332 2.337359 TGCAGGGGTAAGAGTAGGTT 57.663 50.000 0.00 0.00 0.00 3.50
4798 6333 2.337359 TTGCAGGGGTAAGAGTAGGT 57.663 50.000 0.00 0.00 0.00 3.08
4799 6334 2.572104 ACTTTGCAGGGGTAAGAGTAGG 59.428 50.000 2.16 0.00 0.00 3.18
4800 6335 3.600388 CACTTTGCAGGGGTAAGAGTAG 58.400 50.000 2.16 0.00 0.00 2.57
4801 6336 2.290071 GCACTTTGCAGGGGTAAGAGTA 60.290 50.000 2.16 0.00 44.26 2.59
4802 6337 1.545651 GCACTTTGCAGGGGTAAGAGT 60.546 52.381 2.16 0.00 44.26 3.24
4803 6338 1.168714 GCACTTTGCAGGGGTAAGAG 58.831 55.000 2.16 0.00 44.26 2.85
4804 6339 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
4814 6349 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
4815 6350 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
4816 6351 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
4817 6352 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
4818 6353 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
4819 6354 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
4820 6355 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
4821 6356 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
4822 6357 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
4823 6358 0.392193 CGAACCAGCCTCTCTGCATT 60.392 55.000 0.00 0.00 41.50 3.56
4824 6359 1.220206 CGAACCAGCCTCTCTGCAT 59.780 57.895 0.00 0.00 41.50 3.96
4825 6360 1.471829 TTCGAACCAGCCTCTCTGCA 61.472 55.000 0.00 0.00 41.50 4.41
4826 6361 1.016653 GTTCGAACCAGCCTCTCTGC 61.017 60.000 17.68 0.00 41.50 4.26
4827 6362 3.129792 GTTCGAACCAGCCTCTCTG 57.870 57.895 17.68 0.00 42.49 3.35
4838 6373 0.685660 AAGAGGTCCTGGGTTCGAAC 59.314 55.000 20.14 20.14 0.00 3.95
4839 6374 0.685097 CAAGAGGTCCTGGGTTCGAA 59.315 55.000 0.00 0.00 0.00 3.71
4840 6375 1.192146 CCAAGAGGTCCTGGGTTCGA 61.192 60.000 0.00 0.00 30.82 3.71
4841 6376 1.296715 CCAAGAGGTCCTGGGTTCG 59.703 63.158 0.00 0.00 30.82 3.95
4842 6377 1.002011 GCCAAGAGGTCCTGGGTTC 60.002 63.158 0.00 0.00 38.32 3.62
4843 6378 1.774217 TGCCAAGAGGTCCTGGGTT 60.774 57.895 0.00 0.00 38.32 4.11
4844 6379 2.121963 TGCCAAGAGGTCCTGGGT 60.122 61.111 0.00 0.00 38.32 4.51
4845 6380 2.067932 TTGTGCCAAGAGGTCCTGGG 62.068 60.000 0.00 0.00 39.14 4.45
4846 6381 0.607489 CTTGTGCCAAGAGGTCCTGG 60.607 60.000 0.00 0.00 37.19 4.45
4847 6382 0.109342 ACTTGTGCCAAGAGGTCCTG 59.891 55.000 18.22 0.00 37.19 3.86
4848 6383 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
4849 6384 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
4850 6385 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
4851 6386 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
4852 6387 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
4853 6388 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
4854 6389 1.455849 CTCCCCACTTGTGCCAAGA 59.544 57.895 18.22 0.00 0.00 3.02
4855 6390 1.604593 CCTCCCCACTTGTGCCAAG 60.605 63.158 11.87 11.87 0.00 3.61
4856 6391 2.081787 TCCTCCCCACTTGTGCCAA 61.082 57.895 0.00 0.00 0.00 4.52
4857 6392 2.449518 TCCTCCCCACTTGTGCCA 60.450 61.111 0.00 0.00 0.00 4.92
4858 6393 2.034221 GTCCTCCCCACTTGTGCC 59.966 66.667 0.00 0.00 0.00 5.01
4859 6394 0.606673 GAAGTCCTCCCCACTTGTGC 60.607 60.000 0.00 0.00 34.10 4.57
4860 6395 0.764890 TGAAGTCCTCCCCACTTGTG 59.235 55.000 0.00 0.00 34.10 3.33
4861 6396 0.765510 GTGAAGTCCTCCCCACTTGT 59.234 55.000 0.00 0.00 34.10 3.16
4862 6397 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16
4863 6398 0.401395 TGGTGAAGTCCTCCCCACTT 60.401 55.000 0.00 0.00 36.77 3.16
4864 6399 1.128188 GTGGTGAAGTCCTCCCCACT 61.128 60.000 0.00 0.00 41.83 4.00
4865 6400 1.128188 AGTGGTGAAGTCCTCCCCAC 61.128 60.000 0.00 0.00 44.69 4.61
4866 6401 1.127567 CAGTGGTGAAGTCCTCCCCA 61.128 60.000 0.00 0.00 0.00 4.96
4867 6402 1.679898 CAGTGGTGAAGTCCTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
4868 6403 1.003233 GCAGTGGTGAAGTCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
4869 6404 1.374758 CGCAGTGGTGAAGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
4870 6405 2.029844 GCGCAGTGGTGAAGTCCTC 61.030 63.158 0.30 0.00 0.00 3.71
4871 6406 2.031163 GCGCAGTGGTGAAGTCCT 59.969 61.111 0.30 0.00 0.00 3.85
4872 6407 3.050275 GGCGCAGTGGTGAAGTCC 61.050 66.667 10.83 0.00 0.00 3.85
4873 6408 2.280797 TGGCGCAGTGGTGAAGTC 60.281 61.111 10.83 0.00 0.00 3.01
4874 6409 2.281070 CTGGCGCAGTGGTGAAGT 60.281 61.111 10.83 0.00 0.00 3.01
4875 6410 3.052082 CCTGGCGCAGTGGTGAAG 61.052 66.667 10.83 0.00 0.00 3.02
4888 6423 1.004044 CATATAAGAGGGCAGGCCTGG 59.996 57.143 33.46 15.81 36.10 4.45
4889 6424 1.004044 CCATATAAGAGGGCAGGCCTG 59.996 57.143 29.34 29.34 36.10 4.85
4890 6425 1.132397 TCCATATAAGAGGGCAGGCCT 60.132 52.381 17.36 17.36 36.10 5.19
4891 6426 1.003696 GTCCATATAAGAGGGCAGGCC 59.996 57.143 4.33 4.33 0.00 5.19
4892 6427 1.699634 TGTCCATATAAGAGGGCAGGC 59.300 52.381 0.00 0.00 33.91 4.85
4893 6428 5.965033 ATATGTCCATATAAGAGGGCAGG 57.035 43.478 0.00 0.00 43.73 4.85
4894 6429 7.124901 ACACTATATGTCCATATAAGAGGGCAG 59.875 40.741 8.05 0.23 43.73 4.85
4895 6430 6.959954 ACACTATATGTCCATATAAGAGGGCA 59.040 38.462 8.05 0.00 44.75 5.36
4896 6431 7.425224 ACACTATATGTCCATATAAGAGGGC 57.575 40.000 8.05 0.00 36.54 5.19
5022 6743 4.393371 GCCTCTTGTGGAATACTGAAGTTC 59.607 45.833 0.00 0.00 0.00 3.01
5038 6759 9.342308 TCTACAGGAATTTAAATATGCCTCTTG 57.658 33.333 11.98 9.57 0.00 3.02
5039 6760 9.920946 TTCTACAGGAATTTAAATATGCCTCTT 57.079 29.630 11.98 7.10 0.00 2.85
5041 6762 8.568794 GGTTCTACAGGAATTTAAATATGCCTC 58.431 37.037 11.98 2.34 36.24 4.70
5042 6763 7.228706 CGGTTCTACAGGAATTTAAATATGCCT 59.771 37.037 0.01 6.28 36.24 4.75
5043 6764 7.227910 TCGGTTCTACAGGAATTTAAATATGCC 59.772 37.037 0.01 4.08 36.24 4.40
5400 7128 2.953466 TCGGTCCAGTATACACAAGC 57.047 50.000 5.50 0.00 0.00 4.01
5482 7210 5.388408 ACTAGAAAAGGGACTGTAACTCG 57.612 43.478 0.00 0.00 40.86 4.18
5559 7287 3.317603 TGAGTCGACATTGATGCTTGA 57.682 42.857 19.50 0.00 0.00 3.02
5628 7356 4.242811 TGGCTATATCATCCCTTTCAGGT 58.757 43.478 0.00 0.00 31.93 4.00
5945 7674 6.012745 AGAAACCAGTAAGAGCATCCAAATT 58.987 36.000 0.00 0.00 33.66 1.82
6071 7807 9.011095 CCAATACATCTCATCATTAATCTGCTT 57.989 33.333 0.00 0.00 0.00 3.91
6089 7825 5.709631 TGACACTGCACAATAACCAATACAT 59.290 36.000 0.00 0.00 0.00 2.29
6128 7864 6.127647 TGGCAATCCATCAAAGAATAGTCAAC 60.128 38.462 0.00 0.00 37.47 3.18
6233 7969 3.505386 ACCATGAAATGTTGCCTGGTTA 58.495 40.909 0.00 0.00 44.81 2.85
6602 8339 7.391554 AGGCTAATAATATGCACACACCAATAG 59.608 37.037 0.00 0.00 0.00 1.73
6892 8630 6.548622 CCAATAAGATGTGAATCTTCCACCAT 59.451 38.462 4.30 0.00 40.91 3.55
6919 8657 1.071894 CACGAGAGCGACATATTTGCG 60.072 52.381 0.00 0.00 40.01 4.85
7116 8854 6.073440 ACCATGTACAAAGACAAACGATGTAC 60.073 38.462 0.00 7.28 44.12 2.90
7347 9088 3.624861 CCCAGCATGAACTGTATCTGTTC 59.375 47.826 0.00 10.88 39.69 3.18
7439 9187 1.064758 TGGACACTGAGTTGCACCTTT 60.065 47.619 0.00 0.00 0.00 3.11
7440 9188 0.546122 TGGACACTGAGTTGCACCTT 59.454 50.000 0.00 0.00 0.00 3.50
7441 9189 0.767375 ATGGACACTGAGTTGCACCT 59.233 50.000 0.00 0.00 0.00 4.00
7568 9316 3.057386 TGGTGCATAATGCTTGACACAAG 60.057 43.478 7.07 7.07 45.31 3.16
7594 9354 7.910584 AGCAAATCTCCATTGGTAAAGAAAAT 58.089 30.769 1.86 0.00 36.79 1.82
7599 9359 6.071165 AGGAAAGCAAATCTCCATTGGTAAAG 60.071 38.462 1.86 0.00 37.51 1.85
7600 9360 5.779771 AGGAAAGCAAATCTCCATTGGTAAA 59.220 36.000 1.86 0.00 37.51 2.01
7609 9373 2.229784 CACCACAGGAAAGCAAATCTCC 59.770 50.000 0.00 0.00 0.00 3.71
7618 9382 3.154827 ACCAATACCACCACAGGAAAG 57.845 47.619 0.00 0.00 0.00 2.62
7669 9433 4.693566 ACTTGTTACACAACCATATCACGG 59.306 41.667 0.00 0.00 33.96 4.94
7727 9491 5.106197 ACACTTGATCGATTGCAGCATTTTA 60.106 36.000 0.00 0.00 0.00 1.52
7863 9627 1.478510 ACTGTCACTAGATGCCTTCCG 59.521 52.381 0.00 0.00 0.00 4.30
7974 9741 3.648009 GTCTGAGCTAGATACATGGTGC 58.352 50.000 0.00 0.00 37.83 5.01


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

AutoCloner maintained by Alex Coulton.