Multiple sequence alignment - TraesCS1B01G220400

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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 TraesCS1B01G220400 chr1B 100.000 3421 0 0 1 3421 397456289 397452869 0.000000e+00 6318
1 TraesCS1B01G220400 chr6A 94.757 1335 25 9 279 1590 176997708 176996396 0.000000e+00 2036
2 TraesCS1B01G220400 chr6A 98.569 1048 14 1 1587 2634 176995313 176994267 0.000000e+00 1851
3 TraesCS1B01G220400 chr7A 94.603 1334 38 7 279 1590 508021296 508022617 0.000000e+00 2034
4 TraesCS1B01G220400 chr7A 96.949 1049 29 2 1587 2635 508023696 508024741 0.000000e+00 1757
5 TraesCS1B01G220400 chr7A 97.302 630 16 1 962 1590 38918213 38917584 0.000000e+00 1068
6 TraesCS1B01G220400 chr7A 84.318 440 27 13 279 709 38918818 38918412 3.200000e-105 392
7 TraesCS1B01G220400 chr7A 89.873 158 11 5 695 848 38918384 38918228 7.490000e-47 198
8 TraesCS1B01G220400 chr5A 92.188 1344 55 17 278 1590 611836551 611837875 0.000000e+00 1855
9 TraesCS1B01G220400 chr5A 96.483 1052 32 3 1587 2637 611838957 611840004 0.000000e+00 1733
10 TraesCS1B01G220400 chr5A 91.091 1201 53 11 421 1590 6560886 6559709 0.000000e+00 1576
11 TraesCS1B01G220400 chr3B 98.445 1029 16 0 279 1307 52833111 52832083 0.000000e+00 1812
12 TraesCS1B01G220400 chr3B 90.909 110 9 1 276 384 400329799 400329908 2.750000e-31 147
13 TraesCS1B01G220400 chr7B 96.663 1049 33 2 1587 2635 713052050 713053096 0.000000e+00 1742
14 TraesCS1B01G220400 chr7B 95.802 1048 41 2 1587 2634 614616240 614617284 0.000000e+00 1688
15 TraesCS1B01G220400 chr4D 96.670 1051 30 3 1587 2637 9560444 9559399 0.000000e+00 1742
16 TraesCS1B01G220400 chr5B 96.092 1049 38 3 1587 2634 309371017 309372063 0.000000e+00 1707
17 TraesCS1B01G220400 chr5B 95.556 630 27 1 962 1590 309360255 309360884 0.000000e+00 1007
18 TraesCS1B01G220400 chr5B 88.889 108 11 1 279 386 309359524 309359630 7.700000e-27 132
19 TraesCS1B01G220400 chr3A 94.948 1049 46 3 1587 2635 28218322 28217281 0.000000e+00 1637
20 TraesCS1B01G220400 chr3D 94.656 1048 55 1 1587 2634 308054964 308056010 0.000000e+00 1624
21 TraesCS1B01G220400 chr3D 93.082 795 21 12 822 1590 575139115 575139901 0.000000e+00 1133
22 TraesCS1B01G220400 chr1A 91.667 792 49 10 2635 3421 368831699 368830920 0.000000e+00 1081
23 TraesCS1B01G220400 chr1A 92.115 279 6 2 1 279 368831953 368831691 2.490000e-101 379
24 TraesCS1B01G220400 chr4B 96.667 630 20 1 962 1590 483758087 483757458 0.000000e+00 1046
25 TraesCS1B01G220400 chr4B 96.508 630 20 2 962 1590 500050276 500050904 0.000000e+00 1040
26 TraesCS1B01G220400 chr1D 90.629 811 39 16 2635 3421 295973313 295972516 0.000000e+00 1042
27 TraesCS1B01G220400 chr1D 97.133 279 5 3 1 276 295973586 295973308 5.170000e-128 468
28 TraesCS1B01G220400 chr4A 93.175 630 26 4 962 1590 724079707 724080320 0.000000e+00 909
29 TraesCS1B01G220400 chr6D 94.184 533 8 4 278 809 410079487 410079997 0.000000e+00 791
30 TraesCS1B01G220400 chr7D 95.035 141 7 0 279 419 495329357 495329217 4.440000e-54 222


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 TraesCS1B01G220400 chr1B 397452869 397456289 3420 True 6318.000000 6318 100.000000 1 3421 1 chr1B.!!$R1 3420
1 TraesCS1B01G220400 chr6A 176994267 176997708 3441 True 1943.500000 2036 96.663000 279 2634 2 chr6A.!!$R1 2355
2 TraesCS1B01G220400 chr7A 508021296 508024741 3445 False 1895.500000 2034 95.776000 279 2635 2 chr7A.!!$F1 2356
3 TraesCS1B01G220400 chr7A 38917584 38918818 1234 True 552.666667 1068 90.497667 279 1590 3 chr7A.!!$R1 1311
4 TraesCS1B01G220400 chr5A 611836551 611840004 3453 False 1794.000000 1855 94.335500 278 2637 2 chr5A.!!$F1 2359
5 TraesCS1B01G220400 chr5A 6559709 6560886 1177 True 1576.000000 1576 91.091000 421 1590 1 chr5A.!!$R1 1169
6 TraesCS1B01G220400 chr3B 52832083 52833111 1028 True 1812.000000 1812 98.445000 279 1307 1 chr3B.!!$R1 1028
7 TraesCS1B01G220400 chr7B 713052050 713053096 1046 False 1742.000000 1742 96.663000 1587 2635 1 chr7B.!!$F2 1048
8 TraesCS1B01G220400 chr7B 614616240 614617284 1044 False 1688.000000 1688 95.802000 1587 2634 1 chr7B.!!$F1 1047
9 TraesCS1B01G220400 chr4D 9559399 9560444 1045 True 1742.000000 1742 96.670000 1587 2637 1 chr4D.!!$R1 1050
10 TraesCS1B01G220400 chr5B 309371017 309372063 1046 False 1707.000000 1707 96.092000 1587 2634 1 chr5B.!!$F1 1047
11 TraesCS1B01G220400 chr5B 309359524 309360884 1360 False 569.500000 1007 92.222500 279 1590 2 chr5B.!!$F2 1311
12 TraesCS1B01G220400 chr3A 28217281 28218322 1041 True 1637.000000 1637 94.948000 1587 2635 1 chr3A.!!$R1 1048
13 TraesCS1B01G220400 chr3D 308054964 308056010 1046 False 1624.000000 1624 94.656000 1587 2634 1 chr3D.!!$F1 1047
14 TraesCS1B01G220400 chr3D 575139115 575139901 786 False 1133.000000 1133 93.082000 822 1590 1 chr3D.!!$F2 768
15 TraesCS1B01G220400 chr1A 368830920 368831953 1033 True 730.000000 1081 91.891000 1 3421 2 chr1A.!!$R1 3420
16 TraesCS1B01G220400 chr4B 483757458 483758087 629 True 1046.000000 1046 96.667000 962 1590 1 chr4B.!!$R1 628
17 TraesCS1B01G220400 chr4B 500050276 500050904 628 False 1040.000000 1040 96.508000 962 1590 1 chr4B.!!$F1 628
18 TraesCS1B01G220400 chr1D 295972516 295973586 1070 True 755.000000 1042 93.881000 1 3421 2 chr1D.!!$R1 3420
19 TraesCS1B01G220400 chr4A 724079707 724080320 613 False 909.000000 909 93.175000 962 1590 1 chr4A.!!$F1 628
20 TraesCS1B01G220400 chr6D 410079487 410079997 510 False 791.000000 791 94.184000 278 809 1 chr6D.!!$F1 531

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
784 929 1.153127 TTCGTGACGCCCTTTGGTT 60.153 52.632 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2638 5229 0.036765 TACTCCATTGACCACGGTGC 60.037 55.0 1.68 0.0 0.0 5.01 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
276 280 2.626266 CTGTATGTGATACCCCGTAGCA 59.374 50.000 0.00 0.00 34.86 3.49
416 421 3.043419 CCCATCTACTCCCGAGCG 58.957 66.667 0.00 0.00 0.00 5.03
417 422 1.528542 CCCATCTACTCCCGAGCGA 60.529 63.158 0.00 0.00 0.00 4.93
650 706 2.124403 GCCTGGCTGGTGGATCTG 60.124 66.667 12.43 0.00 38.35 2.90
745 890 1.553706 CCCAAGCTTCTGAATGGCTT 58.446 50.000 10.15 10.15 45.57 4.35
784 929 1.153127 TTCGTGACGCCCTTTGGTT 60.153 52.632 0.00 0.00 0.00 3.67
1190 1418 1.278985 TGAAGCAGTCCATTCCGATGT 59.721 47.619 0.00 0.00 0.00 3.06
1700 4101 3.896648 ATGACACTTGTTAGTTTGGCG 57.103 42.857 0.00 0.00 30.26 5.69
1812 4381 8.344939 AGTTCCTTTGTGGGAGGATATTTATA 57.655 34.615 0.00 0.00 42.63 0.98
2301 4890 9.667107 TGAAAAATAAGTTGAGGACTACTATGG 57.333 33.333 0.00 0.00 37.72 2.74
2337 4926 5.231702 TGAATGATTGCTTGGTGACATTTG 58.768 37.500 0.00 0.00 42.32 2.32
2367 4956 4.009675 GGATGTGTTCATGGAAGTAAGCA 58.990 43.478 0.00 0.00 34.06 3.91
2382 4971 8.318412 TGGAAGTAAGCAAAGATGACATAGTTA 58.682 33.333 0.00 0.00 0.00 2.24
2651 5242 4.590487 CGTAGCACCGTGGTCAAT 57.410 55.556 6.48 0.00 0.00 2.57
2652 5243 2.078226 CGTAGCACCGTGGTCAATG 58.922 57.895 6.48 0.00 0.00 2.82
2653 5244 1.358725 CGTAGCACCGTGGTCAATGG 61.359 60.000 6.48 0.00 41.27 3.16
2654 5245 0.036765 GTAGCACCGTGGTCAATGGA 60.037 55.000 6.48 0.00 38.47 3.41
2655 5246 0.249120 TAGCACCGTGGTCAATGGAG 59.751 55.000 6.48 0.00 38.47 3.86
2656 5247 1.302511 GCACCGTGGTCAATGGAGT 60.303 57.895 0.00 0.00 38.47 3.85
2657 5248 0.036765 GCACCGTGGTCAATGGAGTA 60.037 55.000 0.00 0.00 38.47 2.59
2658 5249 1.609580 GCACCGTGGTCAATGGAGTAA 60.610 52.381 0.00 0.00 38.47 2.24
2659 5250 2.939640 GCACCGTGGTCAATGGAGTAAT 60.940 50.000 0.00 0.00 38.47 1.89
2660 5251 3.680475 GCACCGTGGTCAATGGAGTAATA 60.680 47.826 0.00 0.00 38.47 0.98
2661 5252 4.119862 CACCGTGGTCAATGGAGTAATAG 58.880 47.826 0.00 0.00 38.47 1.73
2662 5253 3.773119 ACCGTGGTCAATGGAGTAATAGT 59.227 43.478 0.00 0.00 38.47 2.12
2663 5254 4.957954 ACCGTGGTCAATGGAGTAATAGTA 59.042 41.667 0.00 0.00 38.47 1.82
2664 5255 5.068723 ACCGTGGTCAATGGAGTAATAGTAG 59.931 44.000 0.00 0.00 38.47 2.57
2665 5256 5.068723 CCGTGGTCAATGGAGTAATAGTAGT 59.931 44.000 0.00 0.00 37.06 2.73
2666 5257 6.263842 CCGTGGTCAATGGAGTAATAGTAGTA 59.736 42.308 0.00 0.00 37.06 1.82
2667 5258 7.137426 CGTGGTCAATGGAGTAATAGTAGTAC 58.863 42.308 0.00 0.00 0.00 2.73
2668 5259 7.013083 CGTGGTCAATGGAGTAATAGTAGTACT 59.987 40.741 9.95 9.95 34.46 2.73
2669 5260 9.347240 GTGGTCAATGGAGTAATAGTAGTACTA 57.653 37.037 12.38 12.38 34.82 1.82
2670 5261 9.570468 TGGTCAATGGAGTAATAGTAGTACTAG 57.430 37.037 15.08 0.00 33.66 2.57
2671 5262 9.571816 GGTCAATGGAGTAATAGTAGTACTAGT 57.428 37.037 15.08 14.65 33.66 2.57
2686 5277 9.579932 AGTAGTACTAGTAAACTTGTAACAGGT 57.420 33.333 8.55 0.00 36.32 4.00
2698 5289 9.811995 AAACTTGTAACAGGTTAAATTTCCTTC 57.188 29.630 0.00 0.00 32.63 3.46
2699 5290 8.762481 ACTTGTAACAGGTTAAATTTCCTTCT 57.238 30.769 0.00 0.00 30.91 2.85
2700 5291 9.197306 ACTTGTAACAGGTTAAATTTCCTTCTT 57.803 29.630 0.00 0.00 30.91 2.52
2701 5292 9.678941 CTTGTAACAGGTTAAATTTCCTTCTTC 57.321 33.333 0.00 0.00 30.91 2.87
2702 5293 8.173542 TGTAACAGGTTAAATTTCCTTCTTCC 57.826 34.615 0.00 0.00 30.91 3.46
2703 5294 7.780745 TGTAACAGGTTAAATTTCCTTCTTCCA 59.219 33.333 0.00 0.00 30.91 3.53
2704 5295 7.855784 AACAGGTTAAATTTCCTTCTTCCAT 57.144 32.000 0.00 0.00 30.91 3.41
2705 5296 8.950007 AACAGGTTAAATTTCCTTCTTCCATA 57.050 30.769 0.00 0.00 30.91 2.74
2706 5297 8.581253 ACAGGTTAAATTTCCTTCTTCCATAG 57.419 34.615 0.00 0.00 30.91 2.23
2707 5298 8.170730 ACAGGTTAAATTTCCTTCTTCCATAGT 58.829 33.333 0.00 0.00 30.91 2.12
2708 5299 8.462016 CAGGTTAAATTTCCTTCTTCCATAGTG 58.538 37.037 0.00 0.00 30.91 2.74
2709 5300 8.170730 AGGTTAAATTTCCTTCTTCCATAGTGT 58.829 33.333 0.00 0.00 0.00 3.55
2710 5301 9.457436 GGTTAAATTTCCTTCTTCCATAGTGTA 57.543 33.333 0.00 0.00 0.00 2.90
2719 5310 9.670442 TCCTTCTTCCATAGTGTAATAATAGGT 57.330 33.333 0.00 0.00 0.00 3.08
2738 5329 8.909423 AATAGGTTTAAATTTCCTTCCATGGA 57.091 30.769 11.44 11.44 33.34 3.41
2739 5330 6.605471 AGGTTTAAATTTCCTTCCATGGAC 57.395 37.500 15.91 0.00 35.58 4.02
2740 5331 6.081356 AGGTTTAAATTTCCTTCCATGGACA 58.919 36.000 15.91 5.18 35.58 4.02
2741 5332 6.730507 AGGTTTAAATTTCCTTCCATGGACAT 59.269 34.615 15.91 0.00 35.58 3.06
2742 5333 6.818142 GGTTTAAATTTCCTTCCATGGACATG 59.182 38.462 15.91 7.77 35.58 3.21
2752 5343 2.352422 TGGACATGGAGTGCAGGC 59.648 61.111 0.00 0.00 44.19 4.85
2753 5344 2.226315 TGGACATGGAGTGCAGGCT 61.226 57.895 0.00 0.00 44.19 4.58
2754 5345 1.748122 GGACATGGAGTGCAGGCTG 60.748 63.158 10.94 10.94 38.62 4.85
2755 5346 1.002868 GACATGGAGTGCAGGCTGT 60.003 57.895 17.16 0.00 0.00 4.40
2756 5347 0.250234 GACATGGAGTGCAGGCTGTA 59.750 55.000 17.16 9.18 0.00 2.74
2757 5348 0.914644 ACATGGAGTGCAGGCTGTAT 59.085 50.000 17.16 1.89 0.00 2.29
2758 5349 2.103094 GACATGGAGTGCAGGCTGTATA 59.897 50.000 17.16 0.00 0.00 1.47
2759 5350 2.103771 ACATGGAGTGCAGGCTGTATAG 59.896 50.000 17.16 2.35 0.00 1.31
2760 5351 2.159179 TGGAGTGCAGGCTGTATAGA 57.841 50.000 17.16 0.00 0.00 1.98
2761 5352 2.682594 TGGAGTGCAGGCTGTATAGAT 58.317 47.619 17.16 0.00 0.00 1.98
2762 5353 2.366590 TGGAGTGCAGGCTGTATAGATG 59.633 50.000 17.16 0.00 0.00 2.90
2763 5354 2.366916 GGAGTGCAGGCTGTATAGATGT 59.633 50.000 17.16 0.00 0.00 3.06
2764 5355 3.388308 GAGTGCAGGCTGTATAGATGTG 58.612 50.000 17.16 0.00 0.00 3.21
2765 5356 2.768527 AGTGCAGGCTGTATAGATGTGT 59.231 45.455 17.16 0.00 0.00 3.72
2766 5357 3.960755 AGTGCAGGCTGTATAGATGTGTA 59.039 43.478 17.16 0.00 0.00 2.90
2767 5358 4.405680 AGTGCAGGCTGTATAGATGTGTAA 59.594 41.667 17.16 0.00 0.00 2.41
2768 5359 5.070981 AGTGCAGGCTGTATAGATGTGTAAT 59.929 40.000 17.16 0.00 0.00 1.89
2769 5360 5.178252 GTGCAGGCTGTATAGATGTGTAATG 59.822 44.000 17.16 0.00 0.00 1.90
2770 5361 5.070313 TGCAGGCTGTATAGATGTGTAATGA 59.930 40.000 17.16 0.00 0.00 2.57
2771 5362 5.636965 GCAGGCTGTATAGATGTGTAATGAG 59.363 44.000 17.16 0.00 0.00 2.90
2772 5363 6.517362 GCAGGCTGTATAGATGTGTAATGAGA 60.517 42.308 17.16 0.00 0.00 3.27
2773 5364 6.865726 CAGGCTGTATAGATGTGTAATGAGAC 59.134 42.308 6.28 0.00 0.00 3.36
2774 5365 5.859114 GGCTGTATAGATGTGTAATGAGACG 59.141 44.000 0.00 0.00 0.00 4.18
2775 5366 5.343593 GCTGTATAGATGTGTAATGAGACGC 59.656 44.000 0.00 0.00 0.00 5.19
2776 5367 6.635030 TGTATAGATGTGTAATGAGACGCT 57.365 37.500 0.00 0.00 0.00 5.07
2777 5368 7.039313 TGTATAGATGTGTAATGAGACGCTT 57.961 36.000 0.00 0.00 0.00 4.68
2778 5369 6.918022 TGTATAGATGTGTAATGAGACGCTTG 59.082 38.462 0.00 0.00 0.00 4.01
2779 5370 4.456280 AGATGTGTAATGAGACGCTTGA 57.544 40.909 0.00 0.00 0.00 3.02
2780 5371 5.016051 AGATGTGTAATGAGACGCTTGAT 57.984 39.130 0.00 0.00 0.00 2.57
2781 5372 5.046529 AGATGTGTAATGAGACGCTTGATC 58.953 41.667 0.00 0.00 0.00 2.92
2782 5373 3.179048 TGTGTAATGAGACGCTTGATCG 58.821 45.455 0.00 0.00 0.00 3.69
2783 5374 3.119637 TGTGTAATGAGACGCTTGATCGA 60.120 43.478 0.00 0.00 0.00 3.59
2784 5375 4.045104 GTGTAATGAGACGCTTGATCGAT 58.955 43.478 0.00 0.00 0.00 3.59
2785 5376 4.044426 TGTAATGAGACGCTTGATCGATG 58.956 43.478 0.54 0.00 0.00 3.84
2786 5377 1.495878 ATGAGACGCTTGATCGATGC 58.504 50.000 0.54 0.00 0.00 3.91
2787 5378 0.457443 TGAGACGCTTGATCGATGCT 59.543 50.000 0.54 0.00 0.00 3.79
2788 5379 0.851495 GAGACGCTTGATCGATGCTG 59.149 55.000 0.54 0.00 0.00 4.41
2789 5380 0.174389 AGACGCTTGATCGATGCTGT 59.826 50.000 0.54 3.13 0.00 4.40
2790 5381 1.405463 AGACGCTTGATCGATGCTGTA 59.595 47.619 0.54 0.00 0.00 2.74
2791 5382 2.035193 AGACGCTTGATCGATGCTGTAT 59.965 45.455 0.54 0.00 0.00 2.29
2792 5383 2.398498 ACGCTTGATCGATGCTGTATC 58.602 47.619 0.54 0.00 0.00 2.24
2793 5384 2.035193 ACGCTTGATCGATGCTGTATCT 59.965 45.455 0.54 0.00 33.44 1.98
2794 5385 2.407696 CGCTTGATCGATGCTGTATCTG 59.592 50.000 0.54 0.00 33.44 2.90
2795 5386 2.157279 GCTTGATCGATGCTGTATCTGC 59.843 50.000 0.54 0.00 33.44 4.26
2796 5387 2.445565 TGATCGATGCTGTATCTGCC 57.554 50.000 0.54 0.00 33.44 4.85
2797 5388 1.966354 TGATCGATGCTGTATCTGCCT 59.034 47.619 0.54 0.00 33.44 4.75
2798 5389 3.157087 TGATCGATGCTGTATCTGCCTA 58.843 45.455 0.54 0.00 33.44 3.93
2799 5390 3.766051 TGATCGATGCTGTATCTGCCTAT 59.234 43.478 0.54 0.00 33.44 2.57
2800 5391 3.582714 TCGATGCTGTATCTGCCTATG 57.417 47.619 4.26 0.00 33.44 2.23
2801 5392 2.893489 TCGATGCTGTATCTGCCTATGT 59.107 45.455 4.26 0.00 33.44 2.29
2802 5393 4.079253 TCGATGCTGTATCTGCCTATGTA 58.921 43.478 4.26 0.00 33.44 2.29
2803 5394 4.082733 TCGATGCTGTATCTGCCTATGTAC 60.083 45.833 4.26 0.00 33.44 2.90
2804 5395 4.499183 GATGCTGTATCTGCCTATGTACC 58.501 47.826 0.00 0.00 32.83 3.34
2805 5396 3.304829 TGCTGTATCTGCCTATGTACCA 58.695 45.455 0.00 0.00 0.00 3.25
2806 5397 3.321968 TGCTGTATCTGCCTATGTACCAG 59.678 47.826 0.00 0.00 0.00 4.00
2807 5398 3.322254 GCTGTATCTGCCTATGTACCAGT 59.678 47.826 0.00 0.00 0.00 4.00
2808 5399 4.559704 GCTGTATCTGCCTATGTACCAGTC 60.560 50.000 0.00 0.00 0.00 3.51
2809 5400 4.804597 TGTATCTGCCTATGTACCAGTCT 58.195 43.478 0.00 0.00 0.00 3.24
2810 5401 5.948842 TGTATCTGCCTATGTACCAGTCTA 58.051 41.667 0.00 0.00 0.00 2.59
2811 5402 6.370453 TGTATCTGCCTATGTACCAGTCTAA 58.630 40.000 0.00 0.00 0.00 2.10
2812 5403 6.490381 TGTATCTGCCTATGTACCAGTCTAAG 59.510 42.308 0.00 0.00 0.00 2.18
2813 5404 3.637229 TCTGCCTATGTACCAGTCTAAGC 59.363 47.826 0.00 0.00 0.00 3.09
2814 5405 3.371034 TGCCTATGTACCAGTCTAAGCA 58.629 45.455 0.00 0.00 0.00 3.91
2815 5406 3.384789 TGCCTATGTACCAGTCTAAGCAG 59.615 47.826 0.00 0.00 0.00 4.24
2816 5407 3.385111 GCCTATGTACCAGTCTAAGCAGT 59.615 47.826 0.00 0.00 0.00 4.40
2817 5408 4.500035 GCCTATGTACCAGTCTAAGCAGTC 60.500 50.000 0.00 0.00 0.00 3.51
2818 5409 4.890581 CCTATGTACCAGTCTAAGCAGTCT 59.109 45.833 0.00 0.00 0.00 3.24
2819 5410 4.993029 ATGTACCAGTCTAAGCAGTCTC 57.007 45.455 0.00 0.00 0.00 3.36
2820 5411 2.747989 TGTACCAGTCTAAGCAGTCTCG 59.252 50.000 0.00 0.00 0.00 4.04
2821 5412 1.912417 ACCAGTCTAAGCAGTCTCGT 58.088 50.000 0.00 0.00 0.00 4.18
2822 5413 2.240279 ACCAGTCTAAGCAGTCTCGTT 58.760 47.619 0.00 0.00 0.00 3.85
2823 5414 2.229302 ACCAGTCTAAGCAGTCTCGTTC 59.771 50.000 0.00 0.00 0.00 3.95
2824 5415 2.416162 CCAGTCTAAGCAGTCTCGTTCC 60.416 54.545 0.00 0.00 0.00 3.62
2825 5416 1.819903 AGTCTAAGCAGTCTCGTTCCC 59.180 52.381 0.00 0.00 0.00 3.97
2826 5417 1.544691 GTCTAAGCAGTCTCGTTCCCA 59.455 52.381 0.00 0.00 0.00 4.37
2827 5418 2.029290 GTCTAAGCAGTCTCGTTCCCAA 60.029 50.000 0.00 0.00 0.00 4.12
2828 5419 2.832129 TCTAAGCAGTCTCGTTCCCAAT 59.168 45.455 0.00 0.00 0.00 3.16
2829 5420 4.021229 TCTAAGCAGTCTCGTTCCCAATA 58.979 43.478 0.00 0.00 0.00 1.90
2830 5421 2.674796 AGCAGTCTCGTTCCCAATAC 57.325 50.000 0.00 0.00 0.00 1.89
2831 5422 1.899814 AGCAGTCTCGTTCCCAATACA 59.100 47.619 0.00 0.00 0.00 2.29
2832 5423 2.301870 AGCAGTCTCGTTCCCAATACAA 59.698 45.455 0.00 0.00 0.00 2.41
2833 5424 2.673368 GCAGTCTCGTTCCCAATACAAG 59.327 50.000 0.00 0.00 0.00 3.16
2834 5425 3.864921 GCAGTCTCGTTCCCAATACAAGT 60.865 47.826 0.00 0.00 0.00 3.16
2835 5426 4.619863 GCAGTCTCGTTCCCAATACAAGTA 60.620 45.833 0.00 0.00 0.00 2.24
2836 5427 4.863131 CAGTCTCGTTCCCAATACAAGTAC 59.137 45.833 0.00 0.00 0.00 2.73
2837 5428 4.771054 AGTCTCGTTCCCAATACAAGTACT 59.229 41.667 0.00 0.00 0.00 2.73
2838 5429 5.100943 GTCTCGTTCCCAATACAAGTACTC 58.899 45.833 0.00 0.00 0.00 2.59
2839 5430 4.159135 TCTCGTTCCCAATACAAGTACTCC 59.841 45.833 0.00 0.00 0.00 3.85
2840 5431 3.833650 TCGTTCCCAATACAAGTACTCCA 59.166 43.478 0.00 0.00 0.00 3.86
2841 5432 4.468510 TCGTTCCCAATACAAGTACTCCAT 59.531 41.667 0.00 0.00 0.00 3.41
2842 5433 5.657745 TCGTTCCCAATACAAGTACTCCATA 59.342 40.000 0.00 0.00 0.00 2.74
2843 5434 5.751990 CGTTCCCAATACAAGTACTCCATAC 59.248 44.000 0.00 0.00 0.00 2.39
2844 5435 6.406624 CGTTCCCAATACAAGTACTCCATACT 60.407 42.308 0.00 0.00 46.75 2.12
2845 5436 7.201848 CGTTCCCAATACAAGTACTCCATACTA 60.202 40.741 0.00 0.00 43.79 1.82
2846 5437 7.592885 TCCCAATACAAGTACTCCATACTAC 57.407 40.000 0.00 0.00 43.79 2.73
2847 5438 7.359849 TCCCAATACAAGTACTCCATACTACT 58.640 38.462 0.00 0.00 43.79 2.57
2848 5439 7.842743 TCCCAATACAAGTACTCCATACTACTT 59.157 37.037 0.00 0.00 43.79 2.24
2849 5440 9.139734 CCCAATACAAGTACTCCATACTACTTA 57.860 37.037 0.00 0.00 43.79 2.24
2861 5452 9.877178 ACTCCATACTACTTATTTGTTCTTCAG 57.123 33.333 0.00 0.00 0.00 3.02
2862 5453 9.877178 CTCCATACTACTTATTTGTTCTTCAGT 57.123 33.333 0.00 0.00 0.00 3.41
2863 5454 9.871238 TCCATACTACTTATTTGTTCTTCAGTC 57.129 33.333 0.00 0.00 0.00 3.51
2864 5455 9.099454 CCATACTACTTATTTGTTCTTCAGTCC 57.901 37.037 0.00 0.00 0.00 3.85
2865 5456 9.877178 CATACTACTTATTTGTTCTTCAGTCCT 57.123 33.333 0.00 0.00 0.00 3.85
2866 5457 9.877178 ATACTACTTATTTGTTCTTCAGTCCTG 57.123 33.333 0.00 0.00 0.00 3.86
2867 5458 7.736893 ACTACTTATTTGTTCTTCAGTCCTGT 58.263 34.615 0.00 0.00 0.00 4.00
2868 5459 6.867662 ACTTATTTGTTCTTCAGTCCTGTG 57.132 37.500 0.00 0.00 0.00 3.66
2869 5460 6.357367 ACTTATTTGTTCTTCAGTCCTGTGT 58.643 36.000 0.00 0.00 0.00 3.72
2870 5461 6.828785 ACTTATTTGTTCTTCAGTCCTGTGTT 59.171 34.615 0.00 0.00 0.00 3.32
2871 5462 7.339466 ACTTATTTGTTCTTCAGTCCTGTGTTT 59.661 33.333 0.00 0.00 0.00 2.83
2872 5463 8.740123 TTATTTGTTCTTCAGTCCTGTGTTTA 57.260 30.769 0.00 0.00 0.00 2.01
2873 5464 7.823745 ATTTGTTCTTCAGTCCTGTGTTTAT 57.176 32.000 0.00 0.00 0.00 1.40
2874 5465 7.639113 TTTGTTCTTCAGTCCTGTGTTTATT 57.361 32.000 0.00 0.00 0.00 1.40
2875 5466 7.639113 TTGTTCTTCAGTCCTGTGTTTATTT 57.361 32.000 0.00 0.00 0.00 1.40
2876 5467 7.639113 TGTTCTTCAGTCCTGTGTTTATTTT 57.361 32.000 0.00 0.00 0.00 1.82
2877 5468 7.703328 TGTTCTTCAGTCCTGTGTTTATTTTC 58.297 34.615 0.00 0.00 0.00 2.29
2878 5469 7.556275 TGTTCTTCAGTCCTGTGTTTATTTTCT 59.444 33.333 0.00 0.00 0.00 2.52
2879 5470 7.730364 TCTTCAGTCCTGTGTTTATTTTCTC 57.270 36.000 0.00 0.00 0.00 2.87
2880 5471 7.509546 TCTTCAGTCCTGTGTTTATTTTCTCT 58.490 34.615 0.00 0.00 0.00 3.10
2881 5472 7.442364 TCTTCAGTCCTGTGTTTATTTTCTCTG 59.558 37.037 0.00 0.00 0.00 3.35
2882 5473 6.826668 TCAGTCCTGTGTTTATTTTCTCTGA 58.173 36.000 0.00 0.00 0.00 3.27
2883 5474 7.279615 TCAGTCCTGTGTTTATTTTCTCTGAA 58.720 34.615 0.00 0.00 0.00 3.02
2884 5475 7.773224 TCAGTCCTGTGTTTATTTTCTCTGAAA 59.227 33.333 0.00 0.00 0.00 2.69
2885 5476 8.571336 CAGTCCTGTGTTTATTTTCTCTGAAAT 58.429 33.333 0.00 0.00 33.95 2.17
2886 5477 9.136323 AGTCCTGTGTTTATTTTCTCTGAAATT 57.864 29.630 0.00 0.00 31.96 1.82
2887 5478 9.750125 GTCCTGTGTTTATTTTCTCTGAAATTT 57.250 29.630 0.00 0.00 31.96 1.82
2906 5497 4.664150 TTTTAGCCTTGTTCTGTTTGGG 57.336 40.909 0.00 0.00 0.00 4.12
2907 5498 3.306472 TTAGCCTTGTTCTGTTTGGGT 57.694 42.857 0.00 0.00 0.00 4.51
2909 5500 0.249447 GCCTTGTTCTGTTTGGGTGC 60.249 55.000 0.00 0.00 0.00 5.01
2912 5503 0.394488 TTGTTCTGTTTGGGTGCGGA 60.394 50.000 0.00 0.00 0.00 5.54
2954 5546 2.918934 TCAATTCCCTCCAACCATCTCA 59.081 45.455 0.00 0.00 0.00 3.27
2958 5550 0.179936 CCCTCCAACCATCTCAGAGC 59.820 60.000 0.00 0.00 0.00 4.09
2969 5561 4.099633 CCATCTCAGAGCCTAATCCCATA 58.900 47.826 0.00 0.00 0.00 2.74
2991 5584 3.432252 AGCAAGAGATTGTTAACCGAACG 59.568 43.478 2.48 0.00 41.35 3.95
2998 5591 0.106335 TGTTAACCGAACGAGGCCAA 59.894 50.000 5.01 0.00 41.35 4.52
3004 5597 2.359975 GAACGAGGCCAAGTGGGG 60.360 66.667 5.01 0.00 37.04 4.96
3014 5607 3.884774 AAGTGGGGTCGCTGCCAA 61.885 61.111 0.00 0.00 33.43 4.52
3046 5639 0.313672 CTAGGGCACGAGAGATGCTC 59.686 60.000 0.00 0.00 44.41 4.26
3059 5652 4.203226 AGAGATGCTCTGATTCGTCAGTA 58.797 43.478 5.45 0.00 39.62 2.74
3061 5654 4.677584 AGATGCTCTGATTCGTCAGTAAC 58.322 43.478 5.45 0.00 38.75 2.50
3064 5657 4.237724 TGCTCTGATTCGTCAGTAACTTG 58.762 43.478 5.45 0.00 38.75 3.16
3076 5669 4.023963 GTCAGTAACTTGGAGCAGTTTTCC 60.024 45.833 0.00 0.00 38.07 3.13
3156 5749 4.681978 CCGGCCCTATGCTACCGC 62.682 72.222 0.00 0.00 44.29 5.68
3157 5750 3.616721 CGGCCCTATGCTACCGCT 61.617 66.667 0.00 0.00 39.08 5.52
3158 5751 2.031163 GGCCCTATGCTACCGCTG 59.969 66.667 0.00 0.00 40.92 5.18
3159 5752 2.666526 GCCCTATGCTACCGCTGC 60.667 66.667 0.00 0.00 36.87 5.25
3160 5753 2.356313 CCCTATGCTACCGCTGCG 60.356 66.667 16.34 16.34 36.97 5.18
3161 5754 2.728180 CCTATGCTACCGCTGCGA 59.272 61.111 25.45 2.65 36.97 5.10
3202 5795 1.270777 CGTCGTTGTCGCCTACGTTT 61.271 55.000 0.00 0.00 40.10 3.60
3207 5800 2.431260 GTCGCCTACGTTTGCCGA 60.431 61.111 0.00 0.00 41.18 5.54
3230 5823 1.001706 GGTGGCGTTCTGTTTTCCTTC 60.002 52.381 0.00 0.00 0.00 3.46
3246 5843 0.523072 CTTCGATTGCAACCCTGGTG 59.477 55.000 0.00 0.00 0.00 4.17
3248 5845 1.973281 CGATTGCAACCCTGGTGCT 60.973 57.895 0.00 0.00 0.00 4.40
3269 5866 7.415653 GGTGCTTAATGGATTCTTAACTCCTTG 60.416 40.741 0.00 0.00 32.47 3.61
3271 5868 6.319911 GCTTAATGGATTCTTAACTCCTTGCT 59.680 38.462 0.00 0.00 32.47 3.91
3319 5916 5.122396 CAGCGCCATCCTACTATAAAAATCC 59.878 44.000 2.29 0.00 0.00 3.01
3386 5983 2.232452 GCAGAGGTAAAGAGAGCAGTGA 59.768 50.000 0.00 0.00 0.00 3.41
3387 5984 3.675775 GCAGAGGTAAAGAGAGCAGTGAG 60.676 52.174 0.00 0.00 0.00 3.51
3388 5985 3.509575 CAGAGGTAAAGAGAGCAGTGAGT 59.490 47.826 0.00 0.00 0.00 3.41
3389 5986 3.509575 AGAGGTAAAGAGAGCAGTGAGTG 59.490 47.826 0.00 0.00 0.00 3.51
3390 5987 2.564947 AGGTAAAGAGAGCAGTGAGTGG 59.435 50.000 0.00 0.00 0.00 4.00
3391 5988 2.300437 GGTAAAGAGAGCAGTGAGTGGT 59.700 50.000 0.00 0.00 40.54 4.16
3392 5989 2.540265 AAAGAGAGCAGTGAGTGGTG 57.460 50.000 0.00 0.00 36.87 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.566529 CAGACGCACGTCCTGCTA 59.433 61.111 18.81 0.00 45.59 3.49
276 280 2.045340 GCTGGGTACGCCAATGGT 60.045 61.111 7.55 0.00 36.17 3.55
567 619 1.767692 GGTGGAAGGAGGCAAGGAA 59.232 57.895 0.00 0.00 0.00 3.36
708 853 1.688269 GGCAGCAGCTCCTCATCTCT 61.688 60.000 0.00 0.00 41.70 3.10
745 890 5.453339 CGAACTAGGAATTCAGCAGGGATTA 60.453 44.000 7.93 0.00 0.00 1.75
784 929 2.727123 TGACAGAAGCTCACCCAAAA 57.273 45.000 0.00 0.00 0.00 2.44
1190 1418 9.159364 CATCTTCACAATCACTTTCAATCTCTA 57.841 33.333 0.00 0.00 0.00 2.43
1647 4048 7.983307 ACAATATCTTGATCTCTCTTTTGCAC 58.017 34.615 0.00 0.00 36.20 4.57
1700 4101 5.064452 CCTCATGTGTTGCATTCTACTCTTC 59.936 44.000 0.00 0.00 35.19 2.87
1812 4381 3.707793 GACGTGATCTTCGATTAGGCTT 58.292 45.455 15.29 0.00 0.00 4.35
2301 4890 4.534168 CAATCATTCAAGCGATCATCACC 58.466 43.478 0.00 0.00 0.00 4.02
2382 4971 2.772077 TGCATTGCCATGAAAGCATT 57.228 40.000 6.12 0.00 40.59 3.56
2637 5228 1.003355 CTCCATTGACCACGGTGCT 60.003 57.895 1.68 0.00 0.00 4.40
2638 5229 0.036765 TACTCCATTGACCACGGTGC 60.037 55.000 1.68 0.00 0.00 5.01
2639 5230 2.465860 TTACTCCATTGACCACGGTG 57.534 50.000 0.00 0.00 0.00 4.94
2640 5231 3.773119 ACTATTACTCCATTGACCACGGT 59.227 43.478 0.00 0.00 0.00 4.83
2641 5232 4.402056 ACTATTACTCCATTGACCACGG 57.598 45.455 0.00 0.00 0.00 4.94
2642 5233 6.145338 ACTACTATTACTCCATTGACCACG 57.855 41.667 0.00 0.00 0.00 4.94
2643 5234 8.235359 AGTACTACTATTACTCCATTGACCAC 57.765 38.462 0.00 0.00 0.00 4.16
2644 5235 9.570468 CTAGTACTACTATTACTCCATTGACCA 57.430 37.037 0.00 0.00 31.99 4.02
2645 5236 9.571816 ACTAGTACTACTATTACTCCATTGACC 57.428 37.037 0.00 0.00 31.99 4.02
2660 5251 9.579932 ACCTGTTACAAGTTTACTAGTACTACT 57.420 33.333 0.91 6.57 0.00 2.57
2672 5263 9.811995 GAAGGAAATTTAACCTGTTACAAGTTT 57.188 29.630 4.60 0.00 36.56 2.66
2673 5264 9.197306 AGAAGGAAATTTAACCTGTTACAAGTT 57.803 29.630 4.69 4.69 36.56 2.66
2674 5265 8.762481 AGAAGGAAATTTAACCTGTTACAAGT 57.238 30.769 0.00 0.00 36.56 3.16
2675 5266 9.678941 GAAGAAGGAAATTTAACCTGTTACAAG 57.321 33.333 0.00 0.00 36.56 3.16
2676 5267 8.635328 GGAAGAAGGAAATTTAACCTGTTACAA 58.365 33.333 0.00 0.00 36.56 2.41
2677 5268 7.780745 TGGAAGAAGGAAATTTAACCTGTTACA 59.219 33.333 0.00 1.92 36.56 2.41
2678 5269 8.173542 TGGAAGAAGGAAATTTAACCTGTTAC 57.826 34.615 0.00 0.00 36.56 2.50
2679 5270 8.950007 ATGGAAGAAGGAAATTTAACCTGTTA 57.050 30.769 0.00 0.00 36.56 2.41
2680 5271 7.855784 ATGGAAGAAGGAAATTTAACCTGTT 57.144 32.000 0.00 0.00 36.56 3.16
2681 5272 8.170730 ACTATGGAAGAAGGAAATTTAACCTGT 58.829 33.333 0.00 0.00 36.56 4.00
2682 5273 8.462016 CACTATGGAAGAAGGAAATTTAACCTG 58.538 37.037 0.00 0.00 36.56 4.00
2683 5274 8.170730 ACACTATGGAAGAAGGAAATTTAACCT 58.829 33.333 0.00 0.00 38.23 3.50
2684 5275 8.349568 ACACTATGGAAGAAGGAAATTTAACC 57.650 34.615 0.00 0.00 0.00 2.85
2693 5284 9.670442 ACCTATTATTACACTATGGAAGAAGGA 57.330 33.333 0.00 0.00 23.32 3.36
2712 5303 9.998752 TCCATGGAAGGAAATTTAAACCTATTA 57.001 29.630 13.46 0.00 33.93 0.98
2713 5304 8.758829 GTCCATGGAAGGAAATTTAAACCTATT 58.241 33.333 18.20 0.00 39.92 1.73
2714 5305 7.898636 TGTCCATGGAAGGAAATTTAAACCTAT 59.101 33.333 18.20 0.00 39.92 2.57
2715 5306 7.242359 TGTCCATGGAAGGAAATTTAAACCTA 58.758 34.615 18.20 0.00 39.92 3.08
2716 5307 6.081356 TGTCCATGGAAGGAAATTTAAACCT 58.919 36.000 18.20 0.00 39.92 3.50
2717 5308 6.353404 TGTCCATGGAAGGAAATTTAAACC 57.647 37.500 18.20 0.00 39.92 3.27
2718 5309 7.832503 CATGTCCATGGAAGGAAATTTAAAC 57.167 36.000 18.20 0.00 39.92 2.01
2733 5324 1.381928 GCCTGCACTCCATGTCCATG 61.382 60.000 0.14 0.14 38.51 3.66
2734 5325 1.077212 GCCTGCACTCCATGTCCAT 60.077 57.895 0.00 0.00 0.00 3.41
2735 5326 2.226315 AGCCTGCACTCCATGTCCA 61.226 57.895 0.00 0.00 0.00 4.02
2736 5327 1.748122 CAGCCTGCACTCCATGTCC 60.748 63.158 0.00 0.00 0.00 4.02
2737 5328 0.250234 TACAGCCTGCACTCCATGTC 59.750 55.000 0.00 0.00 0.00 3.06
2738 5329 0.914644 ATACAGCCTGCACTCCATGT 59.085 50.000 0.00 0.00 0.00 3.21
2739 5330 2.366590 TCTATACAGCCTGCACTCCATG 59.633 50.000 0.00 0.00 0.00 3.66
2740 5331 2.682594 TCTATACAGCCTGCACTCCAT 58.317 47.619 0.00 0.00 0.00 3.41
2741 5332 2.159179 TCTATACAGCCTGCACTCCA 57.841 50.000 0.00 0.00 0.00 3.86
2742 5333 2.366916 ACATCTATACAGCCTGCACTCC 59.633 50.000 0.00 0.00 0.00 3.85
2743 5334 3.181471 ACACATCTATACAGCCTGCACTC 60.181 47.826 0.00 0.00 0.00 3.51
2744 5335 2.768527 ACACATCTATACAGCCTGCACT 59.231 45.455 0.00 0.00 0.00 4.40
2745 5336 3.185246 ACACATCTATACAGCCTGCAC 57.815 47.619 0.00 0.00 0.00 4.57
2746 5337 5.070313 TCATTACACATCTATACAGCCTGCA 59.930 40.000 0.00 0.00 0.00 4.41
2747 5338 5.541845 TCATTACACATCTATACAGCCTGC 58.458 41.667 0.00 0.00 0.00 4.85
2748 5339 6.865726 GTCTCATTACACATCTATACAGCCTG 59.134 42.308 0.00 0.00 0.00 4.85
2749 5340 6.294231 CGTCTCATTACACATCTATACAGCCT 60.294 42.308 0.00 0.00 0.00 4.58
2750 5341 5.859114 CGTCTCATTACACATCTATACAGCC 59.141 44.000 0.00 0.00 0.00 4.85
2751 5342 5.343593 GCGTCTCATTACACATCTATACAGC 59.656 44.000 0.00 0.00 0.00 4.40
2752 5343 6.673106 AGCGTCTCATTACACATCTATACAG 58.327 40.000 0.00 0.00 0.00 2.74
2753 5344 6.635030 AGCGTCTCATTACACATCTATACA 57.365 37.500 0.00 0.00 0.00 2.29
2754 5345 7.139392 TCAAGCGTCTCATTACACATCTATAC 58.861 38.462 0.00 0.00 0.00 1.47
2755 5346 7.272037 TCAAGCGTCTCATTACACATCTATA 57.728 36.000 0.00 0.00 0.00 1.31
2756 5347 6.149129 TCAAGCGTCTCATTACACATCTAT 57.851 37.500 0.00 0.00 0.00 1.98
2757 5348 5.576447 TCAAGCGTCTCATTACACATCTA 57.424 39.130 0.00 0.00 0.00 1.98
2758 5349 4.456280 TCAAGCGTCTCATTACACATCT 57.544 40.909 0.00 0.00 0.00 2.90
2759 5350 4.085363 CGATCAAGCGTCTCATTACACATC 60.085 45.833 0.00 0.00 0.00 3.06
2760 5351 3.798878 CGATCAAGCGTCTCATTACACAT 59.201 43.478 0.00 0.00 0.00 3.21
2761 5352 3.119637 TCGATCAAGCGTCTCATTACACA 60.120 43.478 0.00 0.00 0.00 3.72
2762 5353 3.435566 TCGATCAAGCGTCTCATTACAC 58.564 45.455 0.00 0.00 0.00 2.90
2763 5354 3.775661 TCGATCAAGCGTCTCATTACA 57.224 42.857 0.00 0.00 0.00 2.41
2764 5355 3.121194 GCATCGATCAAGCGTCTCATTAC 60.121 47.826 0.00 0.00 0.00 1.89
2765 5356 3.052745 GCATCGATCAAGCGTCTCATTA 58.947 45.455 0.00 0.00 0.00 1.90
2766 5357 1.863454 GCATCGATCAAGCGTCTCATT 59.137 47.619 0.00 0.00 0.00 2.57
2767 5358 1.068281 AGCATCGATCAAGCGTCTCAT 59.932 47.619 0.00 0.00 0.00 2.90
2768 5359 0.457443 AGCATCGATCAAGCGTCTCA 59.543 50.000 0.00 0.00 0.00 3.27
2769 5360 0.851495 CAGCATCGATCAAGCGTCTC 59.149 55.000 0.00 0.00 0.00 3.36
2770 5361 0.174389 ACAGCATCGATCAAGCGTCT 59.826 50.000 0.00 0.00 0.00 4.18
2771 5362 1.840181 TACAGCATCGATCAAGCGTC 58.160 50.000 0.00 0.00 0.00 5.19
2772 5363 2.035193 AGATACAGCATCGATCAAGCGT 59.965 45.455 0.00 2.33 38.81 5.07
2773 5364 2.407696 CAGATACAGCATCGATCAAGCG 59.592 50.000 0.00 0.00 38.81 4.68
2774 5365 2.157279 GCAGATACAGCATCGATCAAGC 59.843 50.000 0.00 0.00 38.81 4.01
2775 5366 2.735663 GGCAGATACAGCATCGATCAAG 59.264 50.000 0.00 0.00 38.81 3.02
2776 5367 2.366590 AGGCAGATACAGCATCGATCAA 59.633 45.455 0.00 0.00 38.81 2.57
2777 5368 1.966354 AGGCAGATACAGCATCGATCA 59.034 47.619 0.00 0.00 38.81 2.92
2778 5369 2.739885 AGGCAGATACAGCATCGATC 57.260 50.000 0.00 0.00 38.81 3.69
2779 5370 3.513119 ACATAGGCAGATACAGCATCGAT 59.487 43.478 0.00 0.00 38.81 3.59
2780 5371 2.893489 ACATAGGCAGATACAGCATCGA 59.107 45.455 0.00 0.00 38.81 3.59
2781 5372 3.309961 ACATAGGCAGATACAGCATCG 57.690 47.619 0.00 0.00 38.81 3.84
2782 5373 4.021104 TGGTACATAGGCAGATACAGCATC 60.021 45.833 0.00 0.00 0.00 3.91
2783 5374 3.903714 TGGTACATAGGCAGATACAGCAT 59.096 43.478 0.00 0.00 0.00 3.79
2784 5375 3.304829 TGGTACATAGGCAGATACAGCA 58.695 45.455 0.00 0.00 0.00 4.41
2785 5376 3.322254 ACTGGTACATAGGCAGATACAGC 59.678 47.826 3.46 0.00 38.20 4.40
2786 5377 4.830046 AGACTGGTACATAGGCAGATACAG 59.170 45.833 5.18 0.00 38.20 2.74
2787 5378 4.804597 AGACTGGTACATAGGCAGATACA 58.195 43.478 5.18 0.00 38.20 2.29
2788 5379 6.570764 GCTTAGACTGGTACATAGGCAGATAC 60.571 46.154 5.18 0.00 38.20 2.24
2789 5380 5.477291 GCTTAGACTGGTACATAGGCAGATA 59.523 44.000 5.18 0.00 38.20 1.98
2790 5381 4.282195 GCTTAGACTGGTACATAGGCAGAT 59.718 45.833 5.18 0.00 38.20 2.90
2791 5382 3.637229 GCTTAGACTGGTACATAGGCAGA 59.363 47.826 5.18 0.00 38.20 4.26
2792 5383 3.384789 TGCTTAGACTGGTACATAGGCAG 59.615 47.826 5.18 0.44 38.20 4.85
2793 5384 3.371034 TGCTTAGACTGGTACATAGGCA 58.629 45.455 5.18 0.90 38.20 4.75
2794 5385 3.385111 ACTGCTTAGACTGGTACATAGGC 59.615 47.826 0.00 0.00 38.20 3.93
2795 5386 4.890581 AGACTGCTTAGACTGGTACATAGG 59.109 45.833 0.00 0.00 38.20 2.57
2796 5387 5.277586 CGAGACTGCTTAGACTGGTACATAG 60.278 48.000 0.00 0.00 38.20 2.23
2797 5388 4.575236 CGAGACTGCTTAGACTGGTACATA 59.425 45.833 0.00 0.00 38.20 2.29
2798 5389 3.378742 CGAGACTGCTTAGACTGGTACAT 59.621 47.826 0.00 0.00 38.20 2.29
2799 5390 2.747989 CGAGACTGCTTAGACTGGTACA 59.252 50.000 0.00 0.00 0.00 2.90
2800 5391 2.748532 ACGAGACTGCTTAGACTGGTAC 59.251 50.000 0.00 0.00 0.00 3.34
2801 5392 3.069079 ACGAGACTGCTTAGACTGGTA 57.931 47.619 0.00 0.00 0.00 3.25
2802 5393 1.912417 ACGAGACTGCTTAGACTGGT 58.088 50.000 0.00 0.00 0.00 4.00
2803 5394 2.416162 GGAACGAGACTGCTTAGACTGG 60.416 54.545 0.00 0.00 0.00 4.00
2804 5395 2.416162 GGGAACGAGACTGCTTAGACTG 60.416 54.545 0.00 0.00 0.00 3.51
2805 5396 1.819903 GGGAACGAGACTGCTTAGACT 59.180 52.381 0.00 0.00 0.00 3.24
2806 5397 1.544691 TGGGAACGAGACTGCTTAGAC 59.455 52.381 0.00 0.00 0.00 2.59
2807 5398 1.919240 TGGGAACGAGACTGCTTAGA 58.081 50.000 0.00 0.00 0.00 2.10
2808 5399 2.743636 TTGGGAACGAGACTGCTTAG 57.256 50.000 0.00 0.00 0.00 2.18
2809 5400 3.512329 TGTATTGGGAACGAGACTGCTTA 59.488 43.478 0.00 0.00 36.86 3.09
2810 5401 2.301870 TGTATTGGGAACGAGACTGCTT 59.698 45.455 0.00 0.00 36.86 3.91
2811 5402 1.899814 TGTATTGGGAACGAGACTGCT 59.100 47.619 0.00 0.00 36.86 4.24
2812 5403 2.380084 TGTATTGGGAACGAGACTGC 57.620 50.000 0.00 0.00 36.86 4.40
2813 5404 3.926616 ACTTGTATTGGGAACGAGACTG 58.073 45.455 0.00 0.00 36.86 3.51
2814 5405 4.771054 AGTACTTGTATTGGGAACGAGACT 59.229 41.667 0.00 0.00 36.86 3.24
2815 5406 5.069501 AGTACTTGTATTGGGAACGAGAC 57.930 43.478 0.00 0.00 36.45 3.36
2816 5407 4.159135 GGAGTACTTGTATTGGGAACGAGA 59.841 45.833 0.00 0.00 33.33 4.04
2817 5408 4.081862 TGGAGTACTTGTATTGGGAACGAG 60.082 45.833 0.00 0.00 34.94 4.18
2818 5409 3.833650 TGGAGTACTTGTATTGGGAACGA 59.166 43.478 0.00 0.00 0.00 3.85
2819 5410 4.196626 TGGAGTACTTGTATTGGGAACG 57.803 45.455 0.00 0.00 0.00 3.95
2820 5411 6.885922 AGTATGGAGTACTTGTATTGGGAAC 58.114 40.000 0.00 0.00 40.80 3.62
2821 5412 7.842743 AGTAGTATGGAGTACTTGTATTGGGAA 59.157 37.037 0.00 0.00 40.80 3.97
2822 5413 7.359849 AGTAGTATGGAGTACTTGTATTGGGA 58.640 38.462 0.00 0.00 40.80 4.37
2823 5414 7.598759 AGTAGTATGGAGTACTTGTATTGGG 57.401 40.000 0.00 0.00 40.80 4.12
2835 5426 9.877178 CTGAAGAACAAATAAGTAGTATGGAGT 57.123 33.333 0.00 0.00 0.00 3.85
2836 5427 9.877178 ACTGAAGAACAAATAAGTAGTATGGAG 57.123 33.333 0.00 0.00 0.00 3.86
2837 5428 9.871238 GACTGAAGAACAAATAAGTAGTATGGA 57.129 33.333 0.00 0.00 0.00 3.41
2838 5429 9.099454 GGACTGAAGAACAAATAAGTAGTATGG 57.901 37.037 0.00 0.00 0.00 2.74
2839 5430 9.877178 AGGACTGAAGAACAAATAAGTAGTATG 57.123 33.333 0.00 0.00 0.00 2.39
2840 5431 9.877178 CAGGACTGAAGAACAAATAAGTAGTAT 57.123 33.333 0.00 0.00 0.00 2.12
2841 5432 8.867097 ACAGGACTGAAGAACAAATAAGTAGTA 58.133 33.333 6.29 0.00 0.00 1.82
2842 5433 7.657761 CACAGGACTGAAGAACAAATAAGTAGT 59.342 37.037 6.29 0.00 0.00 2.73
2843 5434 7.657761 ACACAGGACTGAAGAACAAATAAGTAG 59.342 37.037 6.29 0.00 0.00 2.57
2844 5435 7.506114 ACACAGGACTGAAGAACAAATAAGTA 58.494 34.615 6.29 0.00 0.00 2.24
2845 5436 6.357367 ACACAGGACTGAAGAACAAATAAGT 58.643 36.000 6.29 0.00 0.00 2.24
2846 5437 6.867662 ACACAGGACTGAAGAACAAATAAG 57.132 37.500 6.29 0.00 0.00 1.73
2847 5438 7.639113 AAACACAGGACTGAAGAACAAATAA 57.361 32.000 6.29 0.00 0.00 1.40
2848 5439 8.918202 ATAAACACAGGACTGAAGAACAAATA 57.082 30.769 6.29 0.00 0.00 1.40
2849 5440 7.823745 ATAAACACAGGACTGAAGAACAAAT 57.176 32.000 6.29 0.00 0.00 2.32
2850 5441 7.639113 AATAAACACAGGACTGAAGAACAAA 57.361 32.000 6.29 0.00 0.00 2.83
2851 5442 7.639113 AAATAAACACAGGACTGAAGAACAA 57.361 32.000 6.29 0.00 0.00 2.83
2852 5443 7.556275 AGAAAATAAACACAGGACTGAAGAACA 59.444 33.333 6.29 0.00 0.00 3.18
2853 5444 7.931275 AGAAAATAAACACAGGACTGAAGAAC 58.069 34.615 6.29 0.00 0.00 3.01
2854 5445 7.993183 AGAGAAAATAAACACAGGACTGAAGAA 59.007 33.333 6.29 0.00 0.00 2.52
2855 5446 7.442364 CAGAGAAAATAAACACAGGACTGAAGA 59.558 37.037 6.29 0.00 0.00 2.87
2856 5447 7.442364 TCAGAGAAAATAAACACAGGACTGAAG 59.558 37.037 6.29 0.99 0.00 3.02
2857 5448 7.279615 TCAGAGAAAATAAACACAGGACTGAA 58.720 34.615 6.29 0.00 0.00 3.02
2858 5449 6.826668 TCAGAGAAAATAAACACAGGACTGA 58.173 36.000 6.29 0.00 0.00 3.41
2859 5450 7.496529 TTCAGAGAAAATAAACACAGGACTG 57.503 36.000 0.00 0.00 0.00 3.51
2860 5451 8.697507 ATTTCAGAGAAAATAAACACAGGACT 57.302 30.769 0.00 0.00 0.00 3.85
2861 5452 9.750125 AAATTTCAGAGAAAATAAACACAGGAC 57.250 29.630 0.00 0.00 0.00 3.85
2872 5463 9.481340 GAACAAGGCTAAAATTTCAGAGAAAAT 57.519 29.630 0.00 0.00 0.00 1.82
2873 5464 8.695456 AGAACAAGGCTAAAATTTCAGAGAAAA 58.305 29.630 0.00 0.00 0.00 2.29
2874 5465 8.137437 CAGAACAAGGCTAAAATTTCAGAGAAA 58.863 33.333 0.00 0.00 0.00 2.52
2875 5466 7.285401 ACAGAACAAGGCTAAAATTTCAGAGAA 59.715 33.333 0.00 0.00 0.00 2.87
2876 5467 6.772716 ACAGAACAAGGCTAAAATTTCAGAGA 59.227 34.615 0.00 0.00 0.00 3.10
2877 5468 6.974965 ACAGAACAAGGCTAAAATTTCAGAG 58.025 36.000 0.00 0.00 0.00 3.35
2878 5469 6.959639 ACAGAACAAGGCTAAAATTTCAGA 57.040 33.333 0.00 0.00 0.00 3.27
2879 5470 7.042523 CCAAACAGAACAAGGCTAAAATTTCAG 60.043 37.037 0.00 0.00 0.00 3.02
2880 5471 6.760770 CCAAACAGAACAAGGCTAAAATTTCA 59.239 34.615 0.00 0.00 0.00 2.69
2881 5472 6.202762 CCCAAACAGAACAAGGCTAAAATTTC 59.797 38.462 0.00 0.00 0.00 2.17
2882 5473 6.054941 CCCAAACAGAACAAGGCTAAAATTT 58.945 36.000 0.00 0.00 0.00 1.82
2883 5474 5.130311 ACCCAAACAGAACAAGGCTAAAATT 59.870 36.000 0.00 0.00 0.00 1.82
2884 5475 4.653801 ACCCAAACAGAACAAGGCTAAAAT 59.346 37.500 0.00 0.00 0.00 1.82
2885 5476 4.027437 ACCCAAACAGAACAAGGCTAAAA 58.973 39.130 0.00 0.00 0.00 1.52
2886 5477 3.383185 CACCCAAACAGAACAAGGCTAAA 59.617 43.478 0.00 0.00 0.00 1.85
2887 5478 2.955660 CACCCAAACAGAACAAGGCTAA 59.044 45.455 0.00 0.00 0.00 3.09
2888 5479 2.582052 CACCCAAACAGAACAAGGCTA 58.418 47.619 0.00 0.00 0.00 3.93
2889 5480 1.402787 CACCCAAACAGAACAAGGCT 58.597 50.000 0.00 0.00 0.00 4.58
2933 5525 2.918934 TGAGATGGTTGGAGGGAATTGA 59.081 45.455 0.00 0.00 0.00 2.57
2954 5546 3.582208 CTCTTGCTATGGGATTAGGCTCT 59.418 47.826 0.00 0.00 0.00 4.09
2958 5550 5.874093 ACAATCTCTTGCTATGGGATTAGG 58.126 41.667 0.00 0.00 35.69 2.69
2969 5561 3.432252 CGTTCGGTTAACAATCTCTTGCT 59.568 43.478 8.10 0.00 38.03 3.91
2998 5591 4.335647 CTTGGCAGCGACCCCACT 62.336 66.667 0.00 0.00 0.00 4.00
3023 5616 0.749649 ATCTCTCGTGCCCTAGCTTG 59.250 55.000 0.00 0.00 40.80 4.01
3059 5652 2.629617 CCATGGAAAACTGCTCCAAGTT 59.370 45.455 5.56 0.00 45.96 2.66
3061 5654 2.517959 TCCATGGAAAACTGCTCCAAG 58.482 47.619 13.46 0.00 45.96 3.61
3064 5657 5.221322 GGATTATTCCATGGAAAACTGCTCC 60.221 44.000 30.28 22.85 42.12 4.70
3076 5669 4.109877 AGGAAGCCAGGATTATTCCATG 57.890 45.455 13.01 2.31 45.30 3.66
3156 5749 2.736236 AGCAACTCGCAGTCGCAG 60.736 61.111 2.79 0.00 46.13 5.18
3157 5750 3.037833 CAGCAACTCGCAGTCGCA 61.038 61.111 2.79 0.00 46.13 5.10
3158 5751 3.004734 GACAGCAACTCGCAGTCGC 62.005 63.158 0.00 0.00 45.68 5.19
3159 5752 3.150895 GACAGCAACTCGCAGTCG 58.849 61.111 0.00 0.00 45.68 4.18
3161 5754 1.005630 GGAGACAGCAACTCGCAGT 60.006 57.895 0.00 0.00 44.09 4.40
3207 5800 1.339929 GGAAAACAGAACGCCACCAAT 59.660 47.619 0.00 0.00 0.00 3.16
3230 5823 1.526575 AAGCACCAGGGTTGCAATCG 61.527 55.000 0.59 0.00 35.50 3.34
3246 5843 6.319911 AGCAAGGAGTTAAGAATCCATTAAGC 59.680 38.462 4.57 0.00 38.12 3.09
3248 5845 8.650143 AAAGCAAGGAGTTAAGAATCCATTAA 57.350 30.769 4.57 0.00 38.12 1.40
3269 5866 2.159653 CGCTGTGTTATCCACTGAAAGC 60.160 50.000 3.89 0.00 44.81 3.51
3271 5868 3.064207 GTCGCTGTGTTATCCACTGAAA 58.936 45.455 3.89 0.00 44.81 2.69
3300 5897 4.941873 GGCCGGATTTTTATAGTAGGATGG 59.058 45.833 5.05 0.00 0.00 3.51
3386 5983 2.862541 TCATTGCTAGTTTGCACCACT 58.137 42.857 3.29 3.29 43.20 4.00
3387 5984 3.855689 ATCATTGCTAGTTTGCACCAC 57.144 42.857 0.00 0.00 43.20 4.16
3388 5985 4.202040 GCATATCATTGCTAGTTTGCACCA 60.202 41.667 0.00 0.00 43.20 4.17
3389 5986 4.293415 GCATATCATTGCTAGTTTGCACC 58.707 43.478 0.00 0.00 43.20 5.01
3390 5987 4.293415 GGCATATCATTGCTAGTTTGCAC 58.707 43.478 0.00 0.00 43.20 4.57
3391 5988 3.003585 CGGCATATCATTGCTAGTTTGCA 59.996 43.478 0.00 0.00 42.38 4.08
3392 5989 3.558505 CGGCATATCATTGCTAGTTTGC 58.441 45.455 0.00 0.00 42.38 3.68


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

AutoCloner maintained by Alex Coulton.