Multiple sequence alignment - TraesCS7D01G487600

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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 TraesCS7D01G487600 chr7D 100.000 3158 0 0 1 3158 597685046 597681889 0.000000e+00 5832.0
1 TraesCS7D01G487600 chr7D 82.456 114 8 5 1402 1514 45981030 45980928 4.340000e-14 89.8
2 TraesCS7D01G487600 chr7A 86.982 2604 150 72 292 2841 690361887 690364355 0.000000e+00 2756.0
3 TraesCS7D01G487600 chr7A 89.489 333 32 3 2009 2339 143841230 143841561 4.870000e-113 418.0
4 TraesCS7D01G487600 chr7A 85.526 304 25 11 2 288 690361468 690361769 1.840000e-77 300.0
5 TraesCS7D01G487600 chr7B 91.191 1226 70 18 1396 2599 676411286 676412495 0.000000e+00 1631.0
6 TraesCS7D01G487600 chr7B 90.909 605 14 15 687 1260 676410193 676410787 0.000000e+00 774.0
7 TraesCS7D01G487600 chr7B 91.055 559 43 2 2101 2652 632037009 632036451 0.000000e+00 749.0
8 TraesCS7D01G487600 chr7B 88.889 558 41 11 133 680 676409511 676410057 0.000000e+00 667.0
9 TraesCS7D01G487600 chr7B 96.667 60 2 0 3099 3158 676412653 676412712 2.000000e-17 100.0
10 TraesCS7D01G487600 chr3A 87.453 805 50 19 1138 1922 731695716 731696489 0.000000e+00 880.0
11 TraesCS7D01G487600 chr3A 92.958 71 5 0 1518 1588 216933235 216933305 1.550000e-18 104.0
12 TraesCS7D01G487600 chr3A 92.958 71 5 0 1518 1588 217008665 217008735 1.550000e-18 104.0
13 TraesCS7D01G487600 chr3A 81.579 114 9 5 1402 1514 176234392 176234290 2.020000e-12 84.2
14 TraesCS7D01G487600 chr4B 88.989 663 42 21 746 1393 5537362 5536716 0.000000e+00 791.0
15 TraesCS7D01G487600 chr4B 81.925 852 58 37 1233 2057 656436773 656437555 1.600000e-177 632.0
16 TraesCS7D01G487600 chr4B 85.227 440 53 7 292 727 5537779 5537348 2.890000e-120 442.0
17 TraesCS7D01G487600 chr4B 79.091 220 25 10 1252 1468 232727504 232727705 7.110000e-27 132.0
18 TraesCS7D01G487600 chr1B 82.851 863 51 31 1233 2067 169145870 169145077 0.000000e+00 684.0
19 TraesCS7D01G487600 chr1B 85.070 710 55 24 1302 1989 603632487 603633167 0.000000e+00 676.0
20 TraesCS7D01G487600 chr1B 81.555 862 64 38 1233 2067 546901213 546900420 9.620000e-175 623.0
21 TraesCS7D01G487600 chrUn 85.395 671 56 24 748 1393 60959551 60958898 0.000000e+00 658.0
22 TraesCS7D01G487600 chrUn 85.763 295 28 8 293 581 60960455 60960169 1.840000e-77 300.0
23 TraesCS7D01G487600 chr4A 88.828 546 38 17 748 1291 601197663 601197139 0.000000e+00 649.0
24 TraesCS7D01G487600 chr4A 82.549 510 47 24 1063 1564 444119536 444119061 8.150000e-111 411.0
25 TraesCS7D01G487600 chr6B 82.034 757 50 33 1233 1971 628550325 628551013 1.640000e-157 566.0
26 TraesCS7D01G487600 chr6B 81.212 495 43 23 1578 2058 69398953 69399411 1.390000e-93 353.0
27 TraesCS7D01G487600 chr6B 81.579 114 9 5 1402 1514 711530316 711530214 2.020000e-12 84.2
28 TraesCS7D01G487600 chr5D 84.375 512 38 25 1063 1566 444011890 444011413 6.170000e-127 464.0
29 TraesCS7D01G487600 chr2D 92.429 317 23 1 2024 2339 10247635 10247319 4.800000e-123 451.0
30 TraesCS7D01G487600 chr2D 83.366 511 45 23 1063 1566 131968034 131967557 1.340000e-118 436.0
31 TraesCS7D01G487600 chr2D 91.611 298 22 3 2024 2320 274432397 274432102 2.930000e-110 409.0
32 TraesCS7D01G487600 chr2D 83.871 93 9 3 1402 1493 648847468 648847555 2.020000e-12 84.2
33 TraesCS7D01G487600 chr3D 90.691 333 28 3 2009 2339 443996386 443996717 1.040000e-119 440.0
34 TraesCS7D01G487600 chr1D 86.024 415 28 16 1063 1468 120852241 120851848 4.870000e-113 418.0
35 TraesCS7D01G487600 chr3B 90.221 317 30 1 2024 2339 778204742 778204426 2.270000e-111 412.0
36 TraesCS7D01G487600 chr3B 89.590 317 32 1 2024 2339 778177814 778177498 4.910000e-108 401.0
37 TraesCS7D01G487600 chr3B 82.418 182 26 4 2942 3117 344301227 344301046 1.520000e-33 154.0
38 TraesCS7D01G487600 chr3B 90.909 66 6 0 3018 3083 602757388 602757453 4.340000e-14 89.8
39 TraesCS7D01G487600 chr1A 83.696 92 11 1 1402 1493 198036655 198036742 2.020000e-12 84.2
40 TraesCS7D01G487600 chr1A 82.609 92 12 1 1402 1493 198058578 198058665 9.390000e-11 78.7


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 TraesCS7D01G487600 chr7D 597681889 597685046 3157 True 5832.0 5832 100.000 1 3158 1 chr7D.!!$R2 3157
1 TraesCS7D01G487600 chr7A 690361468 690364355 2887 False 1528.0 2756 86.254 2 2841 2 chr7A.!!$F2 2839
2 TraesCS7D01G487600 chr7B 676409511 676412712 3201 False 793.0 1631 91.914 133 3158 4 chr7B.!!$F1 3025
3 TraesCS7D01G487600 chr7B 632036451 632037009 558 True 749.0 749 91.055 2101 2652 1 chr7B.!!$R1 551
4 TraesCS7D01G487600 chr3A 731695716 731696489 773 False 880.0 880 87.453 1138 1922 1 chr3A.!!$F3 784
5 TraesCS7D01G487600 chr4B 656436773 656437555 782 False 632.0 632 81.925 1233 2057 1 chr4B.!!$F2 824
6 TraesCS7D01G487600 chr4B 5536716 5537779 1063 True 616.5 791 87.108 292 1393 2 chr4B.!!$R1 1101
7 TraesCS7D01G487600 chr1B 169145077 169145870 793 True 684.0 684 82.851 1233 2067 1 chr1B.!!$R1 834
8 TraesCS7D01G487600 chr1B 603632487 603633167 680 False 676.0 676 85.070 1302 1989 1 chr1B.!!$F1 687
9 TraesCS7D01G487600 chr1B 546900420 546901213 793 True 623.0 623 81.555 1233 2067 1 chr1B.!!$R2 834
10 TraesCS7D01G487600 chrUn 60958898 60960455 1557 True 479.0 658 85.579 293 1393 2 chrUn.!!$R1 1100
11 TraesCS7D01G487600 chr4A 601197139 601197663 524 True 649.0 649 88.828 748 1291 1 chr4A.!!$R2 543
12 TraesCS7D01G487600 chr6B 628550325 628551013 688 False 566.0 566 82.034 1233 1971 1 chr6B.!!$F2 738

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
461 592 0.448990 TCTCCGACACCGTTGTATCG 59.551 55.0 0.0 0.0 35.47 2.92 F
799 1560 0.474184 AGGGTTAATGGGCTCGGATG 59.526 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 2559 0.316114 CGCATCACACACACACACAC 60.316 55.0 0.0 0.0 0.0 3.82 R
2719 3966 0.247736 CCCACTGGACTGAGCACTAC 59.752 60.0 0.0 0.0 0.0 2.73 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
53 54 9.899661 TGCACATTTATTGGTAAAGTATAGACT 57.100 29.630 0.00 0.00 37.59 3.24
84 93 9.780413 GATCTTTTCATCAACAAATAAGGTCTC 57.220 33.333 0.00 0.00 0.00 3.36
96 105 7.328737 ACAAATAAGGTCTCAGTACACCATAC 58.671 38.462 3.19 0.00 34.80 2.39
98 107 4.803098 AAGGTCTCAGTACACCATACAC 57.197 45.455 3.19 0.00 34.80 2.90
242 257 6.205658 GCCTATATTTCAACTGGAGATCCAAC 59.794 42.308 2.65 0.00 46.97 3.77
260 275 3.130340 CCAACCACCCTTTTATCGGATTG 59.870 47.826 0.00 0.00 0.00 2.67
387 518 2.978978 TGAGAACCCAGATGACTCCAAA 59.021 45.455 0.00 0.00 0.00 3.28
388 519 3.008375 TGAGAACCCAGATGACTCCAAAG 59.992 47.826 0.00 0.00 0.00 2.77
389 520 2.982488 AGAACCCAGATGACTCCAAAGT 59.018 45.455 0.00 0.00 38.88 2.66
427 558 2.423185 CAGTCTGCCTTGTTGTTTGTCA 59.577 45.455 0.00 0.00 0.00 3.58
428 559 3.088532 AGTCTGCCTTGTTGTTTGTCAA 58.911 40.909 0.00 0.00 0.00 3.18
444 575 2.291282 TGTCAAGGGTTGTGGTTGTTCT 60.291 45.455 0.00 0.00 0.00 3.01
461 592 0.448990 TCTCCGACACCGTTGTATCG 59.551 55.000 0.00 0.00 35.47 2.92
518 655 6.716934 TTGTTGTGGTGTTGTATGGTTATT 57.283 33.333 0.00 0.00 0.00 1.40
551 691 5.508200 TCATTAATTTAATGTGGGACGGC 57.492 39.130 22.35 0.00 44.49 5.68
553 693 5.419155 TCATTAATTTAATGTGGGACGGCAA 59.581 36.000 22.35 3.43 44.49 4.52
625 1254 1.747355 GGAGGTTTCGTACGATGGAGA 59.253 52.381 20.27 0.00 0.00 3.71
626 1255 2.361438 GGAGGTTTCGTACGATGGAGAT 59.639 50.000 20.27 3.37 0.00 2.75
716 1475 5.128008 CGGGGGTGGTTTTTGAATGTATAAT 59.872 40.000 0.00 0.00 0.00 1.28
796 1557 1.148498 GGAGGGTTAATGGGCTCGG 59.852 63.158 0.00 0.00 0.00 4.63
797 1558 1.342672 GGAGGGTTAATGGGCTCGGA 61.343 60.000 0.00 0.00 0.00 4.55
798 1559 0.765510 GAGGGTTAATGGGCTCGGAT 59.234 55.000 0.00 0.00 0.00 4.18
799 1560 0.474184 AGGGTTAATGGGCTCGGATG 59.526 55.000 0.00 0.00 0.00 3.51
834 1595 2.746277 GAACGAGCCCACCGCATT 60.746 61.111 0.00 0.00 41.38 3.56
902 1663 4.186320 TCCGACTTATATACCCCCTCCTA 58.814 47.826 0.00 0.00 0.00 2.94
1009 1789 1.518572 CCGTCAGCCATGGTACGTC 60.519 63.158 24.79 6.88 33.63 4.34
1063 1857 4.803426 CGCGCTGACACCCCTCTC 62.803 72.222 5.56 0.00 0.00 3.20
1064 1858 4.803426 GCGCTGACACCCCTCTCG 62.803 72.222 0.00 0.00 0.00 4.04
1065 1859 4.803426 CGCTGACACCCCTCTCGC 62.803 72.222 0.00 0.00 0.00 5.03
1291 2089 2.711922 CGAGCGCCTCAGGGTAACT 61.712 63.158 2.29 0.00 34.45 2.24
1292 2090 1.381928 CGAGCGCCTCAGGGTAACTA 61.382 60.000 2.29 0.00 34.45 2.24
1293 2091 0.822164 GAGCGCCTCAGGGTAACTAA 59.178 55.000 2.29 0.00 34.45 2.24
1360 2169 2.704572 CTTGCTTTCTTCCCGTGAGAT 58.295 47.619 0.00 0.00 0.00 2.75
1381 2552 3.595190 TTGAGATCTCGGGATGGTAGA 57.405 47.619 17.76 0.00 31.46 2.59
1382 2553 3.816398 TGAGATCTCGGGATGGTAGAT 57.184 47.619 17.76 0.00 32.70 1.98
1385 2556 5.832221 TGAGATCTCGGGATGGTAGATTAT 58.168 41.667 17.76 0.00 30.19 1.28
1386 2557 5.654209 TGAGATCTCGGGATGGTAGATTATG 59.346 44.000 17.76 0.00 30.19 1.90
1387 2558 5.584913 AGATCTCGGGATGGTAGATTATGT 58.415 41.667 0.20 0.00 30.19 2.29
1388 2559 5.420421 AGATCTCGGGATGGTAGATTATGTG 59.580 44.000 0.20 0.00 30.19 3.21
1389 2560 4.480115 TCTCGGGATGGTAGATTATGTGT 58.520 43.478 0.00 0.00 0.00 3.72
1390 2561 4.280929 TCTCGGGATGGTAGATTATGTGTG 59.719 45.833 0.00 0.00 0.00 3.82
1461 2639 2.498167 CTCTGTTTTGGGGTCAGTCAG 58.502 52.381 0.00 0.00 0.00 3.51
1462 2640 1.843851 TCTGTTTTGGGGTCAGTCAGT 59.156 47.619 0.00 0.00 0.00 3.41
1463 2641 2.158813 TCTGTTTTGGGGTCAGTCAGTC 60.159 50.000 0.00 0.00 0.00 3.51
1464 2642 1.562008 TGTTTTGGGGTCAGTCAGTCA 59.438 47.619 0.00 0.00 0.00 3.41
1493 2671 4.971008 CTCTGAACAAGAGCATGAACATG 58.029 43.478 10.04 10.04 45.93 3.21
1615 2816 0.749649 TTTGCTCGGTGTGCCAATTT 59.250 45.000 0.00 0.00 34.09 1.82
1632 2833 7.698130 GTGCCAATTTCATAGTGTCATAGAAAC 59.302 37.037 0.00 0.00 31.81 2.78
1667 2868 4.568072 TTTGACATGTGCAGTATACCCT 57.432 40.909 1.15 0.00 0.00 4.34
1719 2920 6.869913 TGATTCGTAGAGTTAACCGTTGATTT 59.130 34.615 0.88 0.00 38.43 2.17
1720 2921 6.456447 TTCGTAGAGTTAACCGTTGATTTG 57.544 37.500 0.88 0.00 38.43 2.32
1731 2932 5.168647 ACCGTTGATTTGTGGAGGTAATA 57.831 39.130 0.00 0.00 0.00 0.98
1741 2942 3.847184 TGTGGAGGTAATATGGTTGGTCA 59.153 43.478 0.00 0.00 0.00 4.02
1777 2978 1.155889 CAGCAACTTGTCGCCACATA 58.844 50.000 0.00 0.00 30.55 2.29
1822 3039 8.671921 CCTACATGCCTTATTATTAGATTGCAG 58.328 37.037 0.00 0.00 0.00 4.41
1841 3069 1.964223 AGCTGTAGTATCATGGGACGG 59.036 52.381 0.00 0.00 0.00 4.79
1894 3124 9.884465 GTTAACATGGATTAGAACTATTGATGC 57.116 33.333 0.00 0.00 0.00 3.91
1936 3166 2.917713 TTCCCCCTTGCATGTATGTT 57.082 45.000 0.00 0.00 0.00 2.71
1940 3170 1.134729 CCCCTTGCATGTATGTTTGCC 60.135 52.381 0.00 0.00 38.08 4.52
1962 3192 6.122964 GCCCTTCCTATTTGTTATCTCACTT 58.877 40.000 0.00 0.00 0.00 3.16
1963 3193 6.261158 GCCCTTCCTATTTGTTATCTCACTTC 59.739 42.308 0.00 0.00 0.00 3.01
1965 3195 7.829211 CCCTTCCTATTTGTTATCTCACTTCAA 59.171 37.037 0.00 0.00 0.00 2.69
1990 3228 2.100605 ACCGAACTCTTCAGGCATTC 57.899 50.000 0.00 0.00 0.00 2.67
2035 3273 1.004277 TCACCCTGCCTGTGTTTATCC 59.996 52.381 0.00 0.00 35.25 2.59
2219 3457 3.113260 AGACTGAGGTGTTGCTGTTAC 57.887 47.619 0.00 0.00 0.00 2.50
2330 3568 3.001736 GTCAGCGCAATGAAATCTACCTC 59.998 47.826 11.47 0.00 0.00 3.85
2347 3585 8.629821 ATCTACCTCATATATTGCCCTATTGT 57.370 34.615 0.00 0.00 0.00 2.71
2368 3606 5.820131 TGTGTCTTCTTATTTGTTGCTGTG 58.180 37.500 0.00 0.00 0.00 3.66
2418 3656 6.804783 GCAAGTATTTTGTTGCGGTAATAGTT 59.195 34.615 0.00 0.00 39.72 2.24
2429 3667 4.877251 TGCGGTAATAGTTTATGGTTCCAC 59.123 41.667 0.00 0.00 0.00 4.02
2474 3713 2.097142 GTCAAATGATGCTGTGAGGCTC 59.903 50.000 7.79 7.79 0.00 4.70
2475 3714 1.063616 CAAATGATGCTGTGAGGCTCG 59.936 52.381 10.42 0.00 0.00 5.03
2486 3725 1.446272 GAGGCTCGTCTTGTTCGGG 60.446 63.158 0.00 0.00 0.00 5.14
2490 3729 1.080025 CTCGTCTTGTTCGGGGGAC 60.080 63.158 0.00 0.00 0.00 4.46
2516 3755 3.551863 GCTCTTGAGATAGCGCTGTATGT 60.552 47.826 22.90 4.52 0.00 2.29
2524 3764 2.751166 AGCGCTGTATGTTCTTGAGT 57.249 45.000 10.39 0.00 0.00 3.41
2567 3813 6.515272 AGTTTTTATACACCTGCATGAAGG 57.485 37.500 19.21 19.21 43.57 3.46
2600 3846 2.176273 GCCTGGCTGTCGCACATAG 61.176 63.158 12.43 0.00 38.10 2.23
2656 3903 7.775093 TGGCTAGTCTTTGTGCTAAATCATTAT 59.225 33.333 0.00 0.00 0.00 1.28
2662 3909 5.579564 TTGTGCTAAATCATTATGCTGCA 57.420 34.783 4.13 4.13 0.00 4.41
2676 3923 2.241160 TGCTGCATTTGGATGTCTGTT 58.759 42.857 0.00 0.00 35.63 3.16
2677 3924 2.029739 TGCTGCATTTGGATGTCTGTTG 60.030 45.455 0.00 0.00 35.63 3.33
2678 3925 2.673043 GCTGCATTTGGATGTCTGTTGG 60.673 50.000 0.00 0.00 35.63 3.77
2679 3926 1.273048 TGCATTTGGATGTCTGTTGGC 59.727 47.619 0.00 0.00 35.63 4.52
2680 3927 1.404583 GCATTTGGATGTCTGTTGGCC 60.405 52.381 0.00 0.00 35.63 5.36
2681 3928 2.173519 CATTTGGATGTCTGTTGGCCT 58.826 47.619 3.32 0.00 0.00 5.19
2682 3929 1.619654 TTTGGATGTCTGTTGGCCTG 58.380 50.000 3.32 0.00 0.00 4.85
2683 3930 0.478072 TTGGATGTCTGTTGGCCTGT 59.522 50.000 3.32 0.00 0.00 4.00
2684 3931 0.036732 TGGATGTCTGTTGGCCTGTC 59.963 55.000 3.32 0.00 0.00 3.51
2685 3932 1.021390 GGATGTCTGTTGGCCTGTCG 61.021 60.000 3.32 0.00 0.00 4.35
2686 3933 0.037326 GATGTCTGTTGGCCTGTCGA 60.037 55.000 3.32 0.00 0.00 4.20
2702 3949 5.298276 GCCTGTCGAATTGGATTTGGTATTA 59.702 40.000 4.08 0.00 0.00 0.98
2712 3959 3.256631 GGATTTGGTATTAGGCATGCAGG 59.743 47.826 21.36 0.00 0.00 4.85
2719 3966 4.757149 GGTATTAGGCATGCAGGTTTCTAG 59.243 45.833 21.36 0.00 0.00 2.43
2720 3967 4.510167 ATTAGGCATGCAGGTTTCTAGT 57.490 40.909 21.36 4.39 0.00 2.57
2721 3968 5.630415 ATTAGGCATGCAGGTTTCTAGTA 57.370 39.130 21.36 0.00 0.00 1.82
2722 3969 3.550437 AGGCATGCAGGTTTCTAGTAG 57.450 47.619 21.36 0.00 0.00 2.57
2729 3976 3.056536 TGCAGGTTTCTAGTAGTGCTCAG 60.057 47.826 10.12 0.00 0.00 3.35
2746 3993 1.780309 TCAGTCCAGTGGGGTTCATTT 59.220 47.619 9.92 0.00 38.11 2.32
2747 3994 2.176798 TCAGTCCAGTGGGGTTCATTTT 59.823 45.455 9.92 0.00 38.11 1.82
2753 4000 3.694566 CCAGTGGGGTTCATTTTAGTAGC 59.305 47.826 0.00 0.00 0.00 3.58
2757 4004 2.361789 GGGTTCATTTTAGTAGCGCCA 58.638 47.619 2.29 0.00 0.00 5.69
2793 4040 7.386299 GTGCTCAAAGGTATCATAGTTCATAGG 59.614 40.741 0.00 0.00 0.00 2.57
2794 4041 7.290014 TGCTCAAAGGTATCATAGTTCATAGGA 59.710 37.037 0.00 0.00 0.00 2.94
2795 4042 7.816995 GCTCAAAGGTATCATAGTTCATAGGAG 59.183 40.741 0.00 0.00 0.00 3.69
2796 4043 8.195165 TCAAAGGTATCATAGTTCATAGGAGG 57.805 38.462 0.00 0.00 0.00 4.30
2813 4060 7.794683 TCATAGGAGGTATTAACAGGATCCTTT 59.205 37.037 13.00 12.41 37.00 3.11
2820 4067 8.058847 AGGTATTAACAGGATCCTTTTTGCATA 58.941 33.333 18.09 9.75 0.00 3.14
2863 4137 3.699538 TGATTAGCTTAGCTTCTCGTCCA 59.300 43.478 13.44 0.00 40.44 4.02
2871 4145 1.275573 AGCTTCTCGTCCAAAGTACCC 59.724 52.381 0.00 0.00 0.00 3.69
2874 4148 0.883833 TCTCGTCCAAAGTACCCGAC 59.116 55.000 0.00 0.00 0.00 4.79
2889 4163 1.635663 CCGACGCAGGGTCAATCAAC 61.636 60.000 17.21 0.00 46.42 3.18
2897 4171 4.437390 CGCAGGGTCAATCAACTCATTTAC 60.437 45.833 0.00 0.00 0.00 2.01
2898 4172 4.458989 GCAGGGTCAATCAACTCATTTACA 59.541 41.667 0.00 0.00 0.00 2.41
2899 4173 5.126061 GCAGGGTCAATCAACTCATTTACAT 59.874 40.000 0.00 0.00 0.00 2.29
2900 4174 6.350445 GCAGGGTCAATCAACTCATTTACATT 60.350 38.462 0.00 0.00 0.00 2.71
2901 4175 7.605449 CAGGGTCAATCAACTCATTTACATTT 58.395 34.615 0.00 0.00 0.00 2.32
2902 4176 7.543172 CAGGGTCAATCAACTCATTTACATTTG 59.457 37.037 0.00 0.00 0.00 2.32
2903 4177 7.233348 AGGGTCAATCAACTCATTTACATTTGT 59.767 33.333 0.00 0.00 0.00 2.83
2904 4178 7.329226 GGGTCAATCAACTCATTTACATTTGTG 59.671 37.037 0.00 0.00 0.00 3.33
2905 4179 8.081633 GGTCAATCAACTCATTTACATTTGTGA 58.918 33.333 0.00 0.00 0.00 3.58
2906 4180 9.121517 GTCAATCAACTCATTTACATTTGTGAG 57.878 33.333 0.00 0.00 42.80 3.51
2907 4181 7.809331 TCAATCAACTCATTTACATTTGTGAGC 59.191 33.333 0.00 0.00 41.28 4.26
2908 4182 6.882610 TCAACTCATTTACATTTGTGAGCT 57.117 33.333 0.00 0.00 41.28 4.09
2909 4183 6.902341 TCAACTCATTTACATTTGTGAGCTC 58.098 36.000 6.82 6.82 41.28 4.09
2910 4184 5.886960 ACTCATTTACATTTGTGAGCTCC 57.113 39.130 12.15 3.09 41.28 4.70
2911 4185 5.564550 ACTCATTTACATTTGTGAGCTCCT 58.435 37.500 12.15 0.00 41.28 3.69
2912 4186 6.006449 ACTCATTTACATTTGTGAGCTCCTT 58.994 36.000 12.15 0.00 41.28 3.36
2913 4187 6.150140 ACTCATTTACATTTGTGAGCTCCTTC 59.850 38.462 12.15 2.46 41.28 3.46
2914 4188 6.240894 TCATTTACATTTGTGAGCTCCTTCT 58.759 36.000 12.15 0.00 0.00 2.85
2915 4189 5.947228 TTTACATTTGTGAGCTCCTTCTG 57.053 39.130 12.15 5.14 0.00 3.02
2916 4190 2.787994 ACATTTGTGAGCTCCTTCTGG 58.212 47.619 12.15 0.00 0.00 3.86
2917 4191 1.471684 CATTTGTGAGCTCCTTCTGGC 59.528 52.381 12.15 0.00 0.00 4.85
2918 4192 0.767375 TTTGTGAGCTCCTTCTGGCT 59.233 50.000 12.15 0.00 41.88 4.75
2919 4193 1.644509 TTGTGAGCTCCTTCTGGCTA 58.355 50.000 12.15 0.00 39.05 3.93
2920 4194 1.871418 TGTGAGCTCCTTCTGGCTAT 58.129 50.000 12.15 0.00 39.05 2.97
2923 4197 1.062581 TGAGCTCCTTCTGGCTATCCT 60.063 52.381 12.15 0.00 39.05 3.24
2938 4212 4.463879 CCTGCTCCGCACCTCCTG 62.464 72.222 0.00 0.00 33.79 3.86
2961 4235 4.431131 CCCGTTGCTGCATCCCCT 62.431 66.667 1.84 0.00 0.00 4.79
2962 4236 2.825836 CCGTTGCTGCATCCCCTC 60.826 66.667 1.84 0.00 0.00 4.30
2963 4237 2.825836 CGTTGCTGCATCCCCTCC 60.826 66.667 1.84 0.00 0.00 4.30
2964 4238 2.825836 GTTGCTGCATCCCCTCCG 60.826 66.667 1.84 0.00 0.00 4.63
2965 4239 4.113815 TTGCTGCATCCCCTCCGG 62.114 66.667 1.84 0.00 0.00 5.14
2987 4261 2.444706 TCCGAGGGGGAGCTGATG 60.445 66.667 0.00 0.00 40.94 3.07
2988 4262 4.247380 CCGAGGGGGAGCTGATGC 62.247 72.222 0.00 0.00 38.47 3.91
2989 4263 3.473647 CGAGGGGGAGCTGATGCA 61.474 66.667 0.00 0.00 42.74 3.96
2990 4264 2.191641 GAGGGGGAGCTGATGCAC 59.808 66.667 0.00 0.00 42.74 4.57
2991 4265 3.412624 GAGGGGGAGCTGATGCACC 62.413 68.421 0.00 0.00 46.98 5.01
2995 4269 2.045926 GGAGCTGATGCACCGGTT 60.046 61.111 2.97 0.00 39.93 4.44
2996 4270 1.675641 GGAGCTGATGCACCGGTTT 60.676 57.895 2.97 0.00 39.93 3.27
2997 4271 1.503542 GAGCTGATGCACCGGTTTG 59.496 57.895 2.97 0.00 42.74 2.93
2998 4272 1.228245 AGCTGATGCACCGGTTTGT 60.228 52.632 2.97 0.00 42.74 2.83
2999 4273 1.210155 GCTGATGCACCGGTTTGTC 59.790 57.895 2.97 3.32 39.41 3.18
3000 4274 1.497278 CTGATGCACCGGTTTGTCG 59.503 57.895 2.97 0.00 0.00 4.35
3001 4275 0.948623 CTGATGCACCGGTTTGTCGA 60.949 55.000 2.97 0.00 0.00 4.20
3002 4276 0.321210 TGATGCACCGGTTTGTCGAT 60.321 50.000 2.97 0.00 0.00 3.59
3003 4277 1.066787 TGATGCACCGGTTTGTCGATA 60.067 47.619 2.97 0.00 0.00 2.92
3004 4278 2.210116 GATGCACCGGTTTGTCGATAT 58.790 47.619 2.97 0.00 0.00 1.63
3005 4279 2.102070 TGCACCGGTTTGTCGATATT 57.898 45.000 2.97 0.00 0.00 1.28
3006 4280 3.248495 TGCACCGGTTTGTCGATATTA 57.752 42.857 2.97 0.00 0.00 0.98
3007 4281 3.597255 TGCACCGGTTTGTCGATATTAA 58.403 40.909 2.97 0.00 0.00 1.40
3008 4282 4.001652 TGCACCGGTTTGTCGATATTAAA 58.998 39.130 2.97 0.00 0.00 1.52
3009 4283 4.093703 TGCACCGGTTTGTCGATATTAAAG 59.906 41.667 2.97 0.00 0.00 1.85
3010 4284 4.495184 GCACCGGTTTGTCGATATTAAAGG 60.495 45.833 2.97 0.00 0.00 3.11
3011 4285 4.871557 CACCGGTTTGTCGATATTAAAGGA 59.128 41.667 2.97 0.00 0.00 3.36
3012 4286 5.006358 CACCGGTTTGTCGATATTAAAGGAG 59.994 44.000 2.97 0.00 0.00 3.69
3013 4287 4.025145 CCGGTTTGTCGATATTAAAGGAGC 60.025 45.833 0.00 0.00 0.00 4.70
3014 4288 4.025145 CGGTTTGTCGATATTAAAGGAGCC 60.025 45.833 0.00 0.00 0.00 4.70
3015 4289 4.879545 GGTTTGTCGATATTAAAGGAGCCA 59.120 41.667 0.00 0.00 0.00 4.75
3016 4290 5.531287 GGTTTGTCGATATTAAAGGAGCCAT 59.469 40.000 0.00 0.00 0.00 4.40
3017 4291 6.039382 GGTTTGTCGATATTAAAGGAGCCATT 59.961 38.462 0.00 0.00 0.00 3.16
3018 4292 6.618287 TTGTCGATATTAAAGGAGCCATTG 57.382 37.500 0.00 0.00 0.00 2.82
3019 4293 5.063204 TGTCGATATTAAAGGAGCCATTGG 58.937 41.667 0.00 0.00 0.00 3.16
3020 4294 5.163248 TGTCGATATTAAAGGAGCCATTGGA 60.163 40.000 6.95 0.00 0.00 3.53
3021 4295 5.940470 GTCGATATTAAAGGAGCCATTGGAT 59.060 40.000 6.95 0.00 0.00 3.41
3022 4296 5.939883 TCGATATTAAAGGAGCCATTGGATG 59.060 40.000 6.95 0.00 0.00 3.51
3023 4297 5.707298 CGATATTAAAGGAGCCATTGGATGT 59.293 40.000 6.95 0.00 0.00 3.06
3024 4298 6.128172 CGATATTAAAGGAGCCATTGGATGTC 60.128 42.308 6.95 0.00 0.00 3.06
3025 4299 1.755179 AAAGGAGCCATTGGATGTCG 58.245 50.000 6.95 0.00 0.00 4.35
3026 4300 0.749454 AAGGAGCCATTGGATGTCGC 60.749 55.000 6.95 0.00 0.00 5.19
3027 4301 2.189499 GGAGCCATTGGATGTCGCC 61.189 63.158 6.95 0.00 0.00 5.54
3028 4302 2.514592 AGCCATTGGATGTCGCCG 60.515 61.111 6.95 0.00 0.00 6.46
3029 4303 2.513666 GCCATTGGATGTCGCCGA 60.514 61.111 6.95 0.00 0.00 5.54
3030 4304 2.537560 GCCATTGGATGTCGCCGAG 61.538 63.158 6.95 0.00 0.00 4.63
3031 4305 1.143838 CCATTGGATGTCGCCGAGA 59.856 57.895 0.00 0.00 0.00 4.04
3032 4306 0.250038 CCATTGGATGTCGCCGAGAT 60.250 55.000 0.00 0.00 0.00 2.75
3033 4307 1.143305 CATTGGATGTCGCCGAGATC 58.857 55.000 15.22 15.22 32.51 2.75
3034 4308 0.319040 ATTGGATGTCGCCGAGATCG 60.319 55.000 16.71 0.00 33.83 3.69
3035 4309 1.381165 TTGGATGTCGCCGAGATCGA 61.381 55.000 16.71 11.16 43.02 3.59
3039 4313 2.648102 GTCGCCGAGATCGACGTG 60.648 66.667 10.57 0.00 45.11 4.49
3040 4314 3.872728 TCGCCGAGATCGACGTGG 61.873 66.667 10.57 0.00 45.11 4.94
3042 4316 4.194720 GCCGAGATCGACGTGGCT 62.195 66.667 11.36 0.00 43.02 4.75
3043 4317 2.024871 CCGAGATCGACGTGGCTC 59.975 66.667 3.31 0.00 43.02 4.70
3044 4318 2.351322 CGAGATCGACGTGGCTCG 60.351 66.667 17.06 17.06 43.25 5.03
3064 4338 2.115291 GCGATGTTGGGCTCCTTCC 61.115 63.158 0.00 0.00 0.00 3.46
3065 4339 1.815421 CGATGTTGGGCTCCTTCCG 60.815 63.158 0.00 0.00 0.00 4.30
3066 4340 1.452108 GATGTTGGGCTCCTTCCGG 60.452 63.158 0.00 0.00 0.00 5.14
3067 4341 3.645268 ATGTTGGGCTCCTTCCGGC 62.645 63.158 0.00 0.00 0.00 6.13
3068 4342 4.035102 GTTGGGCTCCTTCCGGCT 62.035 66.667 0.00 0.00 0.00 5.52
3069 4343 2.285069 TTGGGCTCCTTCCGGCTA 60.285 61.111 0.00 0.00 0.00 3.93
3070 4344 1.692749 TTGGGCTCCTTCCGGCTAT 60.693 57.895 0.00 0.00 0.00 2.97
3071 4345 1.696097 TTGGGCTCCTTCCGGCTATC 61.696 60.000 0.00 0.00 0.00 2.08
3072 4346 2.744377 GGCTCCTTCCGGCTATCC 59.256 66.667 0.00 0.00 0.00 2.59
3073 4347 2.140792 GGCTCCTTCCGGCTATCCA 61.141 63.158 0.00 0.00 0.00 3.41
3074 4348 1.369321 GCTCCTTCCGGCTATCCAG 59.631 63.158 0.00 0.00 0.00 3.86
3084 4358 3.376218 GCTATCCAGCTCCACACTG 57.624 57.895 0.00 0.00 44.93 3.66
3085 4359 0.813210 GCTATCCAGCTCCACACTGC 60.813 60.000 0.00 0.00 44.93 4.40
3086 4360 0.538584 CTATCCAGCTCCACACTGCA 59.461 55.000 0.00 0.00 33.65 4.41
3087 4361 0.983467 TATCCAGCTCCACACTGCAA 59.017 50.000 0.00 0.00 33.65 4.08
3088 4362 0.111061 ATCCAGCTCCACACTGCAAA 59.889 50.000 0.00 0.00 33.65 3.68
3089 4363 0.535780 TCCAGCTCCACACTGCAAAG 60.536 55.000 0.00 0.00 33.65 2.77
3090 4364 1.285023 CAGCTCCACACTGCAAAGC 59.715 57.895 0.00 0.00 0.00 3.51
3091 4365 1.152902 AGCTCCACACTGCAAAGCA 60.153 52.632 0.00 0.00 35.42 3.91
3092 4366 1.008079 GCTCCACACTGCAAAGCAC 60.008 57.895 0.00 0.00 33.79 4.40
3093 4367 1.727511 GCTCCACACTGCAAAGCACA 61.728 55.000 0.00 0.00 33.79 4.57
3094 4368 0.029834 CTCCACACTGCAAAGCACAC 59.970 55.000 0.00 0.00 33.79 3.82
3095 4369 1.298563 CCACACTGCAAAGCACACG 60.299 57.895 0.00 0.00 33.79 4.49
3096 4370 1.940758 CACACTGCAAAGCACACGC 60.941 57.895 0.00 0.00 33.79 5.34
3097 4371 2.353839 CACTGCAAAGCACACGCC 60.354 61.111 0.00 0.00 39.83 5.68
3152 4426 2.159170 ACAAGCGCTCTTCTGTATCTCC 60.159 50.000 12.06 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.318648 GTCACATACATCTTTGAATGGCCTTA 59.681 38.462 3.32 0.00 0.00 2.69
58 59 9.780413 GAGACCTTATTTGTTGATGAAAAGATC 57.220 33.333 0.00 0.00 0.00 2.75
59 60 9.300681 TGAGACCTTATTTGTTGATGAAAAGAT 57.699 29.630 0.00 0.00 0.00 2.40
60 61 8.690203 TGAGACCTTATTTGTTGATGAAAAGA 57.310 30.769 0.00 0.00 0.00 2.52
61 62 8.571336 ACTGAGACCTTATTTGTTGATGAAAAG 58.429 33.333 0.00 0.00 0.00 2.27
84 93 8.812147 ATAATAATCACGTGTATGGTGTACTG 57.188 34.615 16.51 0.00 36.76 2.74
119 128 8.548877 GGGGTACATGTATCCTATAATCATTGT 58.451 37.037 29.83 0.00 36.56 2.71
120 129 8.548025 TGGGGTACATGTATCCTATAATCATTG 58.452 37.037 29.83 0.00 36.56 2.82
121 130 8.694171 TGGGGTACATGTATCCTATAATCATT 57.306 34.615 29.83 0.00 36.56 2.57
164 173 2.159627 CCCACACGAGCAAACTGTATTC 59.840 50.000 0.00 0.00 0.00 1.75
242 257 1.681264 GCCAATCCGATAAAAGGGTGG 59.319 52.381 0.00 0.00 37.39 4.61
387 518 1.369091 GATGCGGCATCGTTTGGACT 61.369 55.000 25.47 0.00 38.89 3.85
388 519 1.062525 GATGCGGCATCGTTTGGAC 59.937 57.895 25.47 2.83 38.89 4.02
389 520 1.368345 CTGATGCGGCATCGTTTGGA 61.368 55.000 31.17 16.07 43.14 3.53
392 523 0.391661 AGACTGATGCGGCATCGTTT 60.392 50.000 31.17 23.91 43.14 3.60
393 524 1.086067 CAGACTGATGCGGCATCGTT 61.086 55.000 31.17 22.79 43.14 3.85
394 525 1.520120 CAGACTGATGCGGCATCGT 60.520 57.895 31.17 29.28 43.14 3.73
427 558 1.749286 CGGAGAACAACCACAACCCTT 60.749 52.381 0.00 0.00 0.00 3.95
428 559 0.179029 CGGAGAACAACCACAACCCT 60.179 55.000 0.00 0.00 0.00 4.34
474 609 5.295292 ACAAACACACACATGAAAGAGAGAG 59.705 40.000 0.00 0.00 0.00 3.20
484 619 2.922387 CACCACAACAAACACACACATG 59.078 45.455 0.00 0.00 0.00 3.21
485 620 2.560542 ACACCACAACAAACACACACAT 59.439 40.909 0.00 0.00 0.00 3.21
518 655 9.868277 CACATTAAATTAATGAAGCCCTTACAA 57.132 29.630 26.80 0.00 46.52 2.41
625 1254 4.283467 GCAAGGGTGTAAAGGGAAAAGAAT 59.717 41.667 0.00 0.00 0.00 2.40
626 1255 3.639561 GCAAGGGTGTAAAGGGAAAAGAA 59.360 43.478 0.00 0.00 0.00 2.52
689 1318 1.677637 TTCAAAAACCACCCCCGTGC 61.678 55.000 0.00 0.00 38.79 5.34
734 1494 8.506140 TTTGAAGTTTCTTATTTTGCTCGATG 57.494 30.769 0.00 0.00 0.00 3.84
778 1538 1.148498 CCGAGCCCATTAACCCTCC 59.852 63.158 0.00 0.00 0.00 4.30
791 1552 3.330267 GAGTTTATCCATCCATCCGAGC 58.670 50.000 0.00 0.00 0.00 5.03
902 1663 0.692419 AGAGATGGATTGCGGGGAGT 60.692 55.000 0.00 0.00 0.00 3.85
1291 2089 4.884257 GATGGCGAGCGGGCGTTA 62.884 66.667 0.94 0.00 46.04 3.18
1360 2169 3.910989 TCTACCATCCCGAGATCTCAAA 58.089 45.455 22.31 7.29 0.00 2.69
1381 2552 4.195416 TCACACACACACACACACATAAT 58.805 39.130 0.00 0.00 0.00 1.28
1382 2553 3.600388 TCACACACACACACACACATAA 58.400 40.909 0.00 0.00 0.00 1.90
1385 2556 1.736681 CATCACACACACACACACACA 59.263 47.619 0.00 0.00 0.00 3.72
1386 2557 1.531677 GCATCACACACACACACACAC 60.532 52.381 0.00 0.00 0.00 3.82
1387 2558 0.731994 GCATCACACACACACACACA 59.268 50.000 0.00 0.00 0.00 3.72
1388 2559 0.316114 CGCATCACACACACACACAC 60.316 55.000 0.00 0.00 0.00 3.82
1389 2560 2.013021 CGCATCACACACACACACA 58.987 52.632 0.00 0.00 0.00 3.72
1390 2561 1.369209 GCGCATCACACACACACAC 60.369 57.895 0.30 0.00 0.00 3.82
1493 2671 9.655769 CAATTCATAACACAATCATACAGTAGC 57.344 33.333 0.00 0.00 0.00 3.58
1499 2679 7.596248 GGCATCCAATTCATAACACAATCATAC 59.404 37.037 0.00 0.00 0.00 2.39
1615 2816 6.036577 TGTGCAGTTTCTATGACACTATGA 57.963 37.500 0.00 0.00 0.00 2.15
1632 2833 5.344933 CACATGTCAAAATCAGATTGTGCAG 59.655 40.000 8.34 6.90 30.62 4.41
1667 2868 6.040955 TGGTGATGCCAAATTACACTAAACAA 59.959 34.615 0.00 0.00 45.94 2.83
1719 2920 3.847184 TGACCAACCATATTACCTCCACA 59.153 43.478 0.00 0.00 0.00 4.17
1720 2921 4.497291 TGACCAACCATATTACCTCCAC 57.503 45.455 0.00 0.00 0.00 4.02
1731 2932 2.596346 TCAACAGCATTGACCAACCAT 58.404 42.857 0.00 0.00 0.00 3.55
1761 2962 2.162208 AGCAATATGTGGCGACAAGTTG 59.838 45.455 18.68 18.68 46.06 3.16
1777 2978 1.968017 CACAGCCGTGGACAGCAAT 60.968 57.895 0.00 0.00 39.64 3.56
1822 3039 1.961394 TCCGTCCCATGATACTACAGC 59.039 52.381 0.00 0.00 0.00 4.40
1841 3069 7.534085 TTCATAGACCGACAACATATGTTTC 57.466 36.000 18.50 16.47 44.12 2.78
1936 3166 5.885912 GTGAGATAACAAATAGGAAGGGCAA 59.114 40.000 0.00 0.00 0.00 4.52
1940 3170 8.792830 TTGAAGTGAGATAACAAATAGGAAGG 57.207 34.615 0.00 0.00 0.00 3.46
1962 3192 5.048991 GCCTGAAGAGTTCGGTTTAAATTGA 60.049 40.000 0.00 0.00 34.15 2.57
1963 3193 5.154222 GCCTGAAGAGTTCGGTTTAAATTG 58.846 41.667 0.00 0.00 34.15 2.32
1965 3195 4.394729 TGCCTGAAGAGTTCGGTTTAAAT 58.605 39.130 0.00 0.00 34.15 1.40
1990 3228 1.518325 TCGGGTTTGTAGTGTGCATG 58.482 50.000 0.00 0.00 0.00 4.06
2035 3273 1.003355 ACCCGTTGATCTGCAGGTG 60.003 57.895 15.13 0.00 0.00 4.00
2219 3457 4.637534 CCCTGGACATAGTGAACTTGAATG 59.362 45.833 0.00 0.00 0.00 2.67
2330 3568 8.627208 AAGAAGACACAATAGGGCAATATATG 57.373 34.615 0.00 0.00 0.00 1.78
2347 3585 4.337836 TGCACAGCAACAAATAAGAAGACA 59.662 37.500 0.00 0.00 34.76 3.41
2368 3606 1.623973 GGAACAACCGTAGAGCGTGC 61.624 60.000 0.00 0.00 39.32 5.34
2415 3653 3.371166 CCATACCCGTGGAACCATAAACT 60.371 47.826 0.00 0.00 42.02 2.66
2418 3656 2.479340 TCCATACCCGTGGAACCATAA 58.521 47.619 0.00 0.00 45.03 1.90
2429 3667 5.007626 CACAAACATGATAACTCCATACCCG 59.992 44.000 0.00 0.00 0.00 5.28
2474 3713 1.070105 TTGTCCCCCGAACAAGACG 59.930 57.895 0.00 0.00 32.98 4.18
2486 3725 2.484594 GCTATCTCAAGAGCCTTGTCCC 60.485 54.545 12.71 0.00 33.50 4.46
2490 3729 1.202510 AGCGCTATCTCAAGAGCCTTG 60.203 52.381 8.99 8.22 42.57 3.61
2516 3755 5.163364 GGCTATCTCAAGATCCACTCAAGAA 60.163 44.000 0.00 0.00 36.05 2.52
2524 3764 4.809193 ACTACAGGCTATCTCAAGATCCA 58.191 43.478 0.00 0.00 36.05 3.41
2567 3813 0.967380 CAGGCATCAAGAACACCCCC 60.967 60.000 0.00 0.00 0.00 5.40
2582 3828 2.125147 TATGTGCGACAGCCAGGC 60.125 61.111 1.84 1.84 44.33 4.85
2600 3846 1.094785 ACAGAGTTGTGTTGTGGTGC 58.905 50.000 0.00 0.00 35.83 5.01
2637 3884 6.127675 TGCAGCATAATGATTTAGCACAAAGA 60.128 34.615 0.00 0.00 0.00 2.52
2656 3903 1.913778 ACAGACATCCAAATGCAGCA 58.086 45.000 0.00 0.00 36.26 4.41
2662 3909 2.173519 CAGGCCAACAGACATCCAAAT 58.826 47.619 5.01 0.00 0.00 2.32
2676 3923 1.818060 CAAATCCAATTCGACAGGCCA 59.182 47.619 5.01 0.00 0.00 5.36
2677 3924 1.134946 CCAAATCCAATTCGACAGGCC 59.865 52.381 0.00 0.00 0.00 5.19
2678 3925 1.818674 ACCAAATCCAATTCGACAGGC 59.181 47.619 0.00 0.00 0.00 4.85
2679 3926 5.835113 AATACCAAATCCAATTCGACAGG 57.165 39.130 0.00 0.00 0.00 4.00
2680 3927 6.513393 GCCTAATACCAAATCCAATTCGACAG 60.513 42.308 0.00 0.00 0.00 3.51
2681 3928 5.298276 GCCTAATACCAAATCCAATTCGACA 59.702 40.000 0.00 0.00 0.00 4.35
2682 3929 5.298276 TGCCTAATACCAAATCCAATTCGAC 59.702 40.000 0.00 0.00 0.00 4.20
2683 3930 5.441500 TGCCTAATACCAAATCCAATTCGA 58.558 37.500 0.00 0.00 0.00 3.71
2684 3931 5.766150 TGCCTAATACCAAATCCAATTCG 57.234 39.130 0.00 0.00 0.00 3.34
2685 3932 5.928264 GCATGCCTAATACCAAATCCAATTC 59.072 40.000 6.36 0.00 0.00 2.17
2686 3933 5.366186 TGCATGCCTAATACCAAATCCAATT 59.634 36.000 16.68 0.00 0.00 2.32
2702 3949 2.840651 ACTACTAGAAACCTGCATGCCT 59.159 45.455 16.68 6.16 0.00 4.75
2712 3959 4.218852 ACTGGACTGAGCACTACTAGAAAC 59.781 45.833 0.00 0.00 0.00 2.78
2719 3966 0.247736 CCCACTGGACTGAGCACTAC 59.752 60.000 0.00 0.00 0.00 2.73
2720 3967 0.904865 CCCCACTGGACTGAGCACTA 60.905 60.000 0.00 0.00 35.39 2.74
2721 3968 2.219875 CCCCACTGGACTGAGCACT 61.220 63.158 0.00 0.00 35.39 4.40
2722 3969 2.056906 AACCCCACTGGACTGAGCAC 62.057 60.000 0.00 0.00 38.00 4.40
2729 3976 3.763057 ACTAAAATGAACCCCACTGGAC 58.237 45.455 0.00 0.00 38.00 4.02
2746 3993 2.465860 TTCTTGCTTGGCGCTACTAA 57.534 45.000 7.64 0.00 40.11 2.24
2747 3994 2.289444 ACTTTCTTGCTTGGCGCTACTA 60.289 45.455 7.64 0.00 40.11 1.82
2753 4000 4.233408 GCACTTTCTTGCTTGGCG 57.767 55.556 0.00 0.00 39.59 5.69
2793 4040 6.377146 TGCAAAAAGGATCCTGTTAATACCTC 59.623 38.462 17.95 3.34 0.00 3.85
2794 4041 6.252995 TGCAAAAAGGATCCTGTTAATACCT 58.747 36.000 17.95 0.00 0.00 3.08
2795 4042 6.524101 TGCAAAAAGGATCCTGTTAATACC 57.476 37.500 17.95 5.50 0.00 2.73
2837 4084 6.392625 ACGAGAAGCTAAGCTAATCACATA 57.607 37.500 0.00 0.00 38.25 2.29
2841 4088 3.699538 TGGACGAGAAGCTAAGCTAATCA 59.300 43.478 0.00 0.00 38.25 2.57
2842 4089 4.308899 TGGACGAGAAGCTAAGCTAATC 57.691 45.455 0.00 0.00 38.25 1.75
2843 4090 4.737855 TTGGACGAGAAGCTAAGCTAAT 57.262 40.909 0.00 0.00 38.25 1.73
2844 4091 4.021368 ACTTTGGACGAGAAGCTAAGCTAA 60.021 41.667 0.00 0.00 38.25 3.09
2846 4093 2.300437 ACTTTGGACGAGAAGCTAAGCT 59.700 45.455 0.00 0.00 42.56 3.74
2847 4094 2.689646 ACTTTGGACGAGAAGCTAAGC 58.310 47.619 0.00 0.00 0.00 3.09
2848 4095 4.174762 GGTACTTTGGACGAGAAGCTAAG 58.825 47.826 0.00 0.00 0.00 2.18
2851 4098 1.275573 GGGTACTTTGGACGAGAAGCT 59.724 52.381 0.00 0.00 0.00 3.74
2852 4099 1.723220 GGGTACTTTGGACGAGAAGC 58.277 55.000 0.00 0.00 0.00 3.86
2853 4100 1.542915 TCGGGTACTTTGGACGAGAAG 59.457 52.381 0.00 0.00 0.00 2.85
2855 4102 0.883833 GTCGGGTACTTTGGACGAGA 59.116 55.000 0.00 0.00 33.92 4.04
2863 4137 2.660802 CCCTGCGTCGGGTACTTT 59.339 61.111 3.28 0.00 39.51 2.66
2871 4145 0.670546 AGTTGATTGACCCTGCGTCG 60.671 55.000 0.00 0.00 45.23 5.12
2874 4148 1.742761 ATGAGTTGATTGACCCTGCG 58.257 50.000 0.00 0.00 0.00 5.18
2889 4163 6.373774 AGAAGGAGCTCACAAATGTAAATGAG 59.626 38.462 17.19 0.00 41.29 2.90
2897 4171 1.471684 GCCAGAAGGAGCTCACAAATG 59.528 52.381 17.19 7.10 36.89 2.32
2898 4172 1.353694 AGCCAGAAGGAGCTCACAAAT 59.646 47.619 17.19 0.00 32.71 2.32
2899 4173 0.767375 AGCCAGAAGGAGCTCACAAA 59.233 50.000 17.19 0.00 32.71 2.83
2900 4174 1.644509 TAGCCAGAAGGAGCTCACAA 58.355 50.000 17.19 0.00 40.56 3.33
2901 4175 1.759445 GATAGCCAGAAGGAGCTCACA 59.241 52.381 17.19 0.00 40.56 3.58
2902 4176 1.069978 GGATAGCCAGAAGGAGCTCAC 59.930 57.143 17.19 5.01 40.56 3.51
2903 4177 1.062581 AGGATAGCCAGAAGGAGCTCA 60.063 52.381 17.19 0.00 40.56 4.26
2904 4178 1.344114 CAGGATAGCCAGAAGGAGCTC 59.656 57.143 4.71 4.71 40.56 4.09
2905 4179 1.422531 CAGGATAGCCAGAAGGAGCT 58.577 55.000 0.00 0.00 43.20 4.09
2906 4180 0.250252 GCAGGATAGCCAGAAGGAGC 60.250 60.000 0.00 0.00 36.89 4.70
2907 4181 1.344114 GAGCAGGATAGCCAGAAGGAG 59.656 57.143 0.00 0.00 36.89 3.69
2908 4182 1.418334 GAGCAGGATAGCCAGAAGGA 58.582 55.000 0.00 0.00 36.89 3.36
2909 4183 0.396060 GGAGCAGGATAGCCAGAAGG 59.604 60.000 0.00 0.00 36.29 3.46
2910 4184 0.033228 CGGAGCAGGATAGCCAGAAG 59.967 60.000 0.00 0.00 36.29 2.85
2911 4185 2.127839 CGGAGCAGGATAGCCAGAA 58.872 57.895 0.00 0.00 36.29 3.02
2912 4186 3.862142 CGGAGCAGGATAGCCAGA 58.138 61.111 0.00 0.00 36.29 3.86
2944 4218 4.431131 AGGGGATGCAGCAACGGG 62.431 66.667 3.51 0.00 0.00 5.28
2945 4219 2.825836 GAGGGGATGCAGCAACGG 60.826 66.667 3.51 0.00 0.00 4.44
2946 4220 2.825836 GGAGGGGATGCAGCAACG 60.826 66.667 3.51 0.00 0.00 4.10
2947 4221 2.825836 CGGAGGGGATGCAGCAAC 60.826 66.667 3.51 0.00 0.00 4.17
2970 4244 2.444706 CATCAGCTCCCCCTCGGA 60.445 66.667 0.00 0.00 38.83 4.55
2971 4245 4.247380 GCATCAGCTCCCCCTCGG 62.247 72.222 0.00 0.00 37.91 4.63
2972 4246 3.473647 TGCATCAGCTCCCCCTCG 61.474 66.667 0.00 0.00 42.74 4.63
2973 4247 2.191641 GTGCATCAGCTCCCCCTC 59.808 66.667 0.00 0.00 42.74 4.30
2974 4248 3.415087 GGTGCATCAGCTCCCCCT 61.415 66.667 0.00 0.00 46.24 4.79
2979 4253 1.237285 ACAAACCGGTGCATCAGCTC 61.237 55.000 8.52 0.00 42.74 4.09
2980 4254 1.228245 ACAAACCGGTGCATCAGCT 60.228 52.632 8.52 0.00 42.74 4.24
2981 4255 1.210155 GACAAACCGGTGCATCAGC 59.790 57.895 8.52 0.00 42.57 4.26
2982 4256 0.948623 TCGACAAACCGGTGCATCAG 60.949 55.000 8.52 0.00 0.00 2.90
2983 4257 0.321210 ATCGACAAACCGGTGCATCA 60.321 50.000 8.52 0.00 0.00 3.07
2984 4258 1.647346 TATCGACAAACCGGTGCATC 58.353 50.000 8.52 4.86 0.00 3.91
2985 4259 2.325583 ATATCGACAAACCGGTGCAT 57.674 45.000 8.52 0.00 0.00 3.96
2986 4260 2.102070 AATATCGACAAACCGGTGCA 57.898 45.000 8.52 0.00 0.00 4.57
2987 4261 4.495184 CCTTTAATATCGACAAACCGGTGC 60.495 45.833 8.52 0.00 0.00 5.01
2988 4262 4.871557 TCCTTTAATATCGACAAACCGGTG 59.128 41.667 8.52 0.00 0.00 4.94
2989 4263 5.088680 TCCTTTAATATCGACAAACCGGT 57.911 39.130 0.00 0.00 0.00 5.28
2990 4264 4.025145 GCTCCTTTAATATCGACAAACCGG 60.025 45.833 0.00 0.00 0.00 5.28
2991 4265 4.025145 GGCTCCTTTAATATCGACAAACCG 60.025 45.833 0.00 0.00 0.00 4.44
2992 4266 4.879545 TGGCTCCTTTAATATCGACAAACC 59.120 41.667 0.00 0.00 0.00 3.27
2993 4267 6.619801 ATGGCTCCTTTAATATCGACAAAC 57.380 37.500 0.00 0.00 0.00 2.93
2994 4268 6.039270 CCAATGGCTCCTTTAATATCGACAAA 59.961 38.462 0.00 0.00 0.00 2.83
2995 4269 5.530915 CCAATGGCTCCTTTAATATCGACAA 59.469 40.000 0.00 0.00 0.00 3.18
2996 4270 5.063204 CCAATGGCTCCTTTAATATCGACA 58.937 41.667 0.00 0.00 0.00 4.35
2997 4271 5.305585 TCCAATGGCTCCTTTAATATCGAC 58.694 41.667 0.00 0.00 0.00 4.20
2998 4272 5.560722 TCCAATGGCTCCTTTAATATCGA 57.439 39.130 0.00 0.00 0.00 3.59
2999 4273 5.707298 ACATCCAATGGCTCCTTTAATATCG 59.293 40.000 0.00 0.00 33.60 2.92
3000 4274 6.128172 CGACATCCAATGGCTCCTTTAATATC 60.128 42.308 0.00 0.00 35.65 1.63
3001 4275 5.707298 CGACATCCAATGGCTCCTTTAATAT 59.293 40.000 0.00 0.00 35.65 1.28
3002 4276 5.063204 CGACATCCAATGGCTCCTTTAATA 58.937 41.667 0.00 0.00 35.65 0.98
3003 4277 3.885297 CGACATCCAATGGCTCCTTTAAT 59.115 43.478 0.00 0.00 35.65 1.40
3004 4278 3.278574 CGACATCCAATGGCTCCTTTAA 58.721 45.455 0.00 0.00 35.65 1.52
3005 4279 2.917933 CGACATCCAATGGCTCCTTTA 58.082 47.619 0.00 0.00 35.65 1.85
3006 4280 1.755179 CGACATCCAATGGCTCCTTT 58.245 50.000 0.00 0.00 35.65 3.11
3007 4281 0.749454 GCGACATCCAATGGCTCCTT 60.749 55.000 0.00 0.00 35.65 3.36
3008 4282 1.153086 GCGACATCCAATGGCTCCT 60.153 57.895 0.00 0.00 35.65 3.69
3009 4283 2.189499 GGCGACATCCAATGGCTCC 61.189 63.158 0.00 0.00 35.74 4.70
3010 4284 2.537560 CGGCGACATCCAATGGCTC 61.538 63.158 0.00 0.00 35.65 4.70
3011 4285 2.514592 CGGCGACATCCAATGGCT 60.515 61.111 0.00 0.00 35.65 4.75
3012 4286 2.513666 TCGGCGACATCCAATGGC 60.514 61.111 4.99 0.00 33.97 4.40
3013 4287 0.250038 ATCTCGGCGACATCCAATGG 60.250 55.000 4.99 0.00 33.60 3.16
3014 4288 1.143305 GATCTCGGCGACATCCAATG 58.857 55.000 13.33 0.00 0.00 2.82
3015 4289 0.319040 CGATCTCGGCGACATCCAAT 60.319 55.000 17.56 0.60 35.37 3.16
3016 4290 1.065764 CGATCTCGGCGACATCCAA 59.934 57.895 17.56 0.00 35.37 3.53
3017 4291 1.822186 TCGATCTCGGCGACATCCA 60.822 57.895 17.56 4.06 40.29 3.41
3018 4292 3.031495 TCGATCTCGGCGACATCC 58.969 61.111 17.56 2.83 40.29 3.51
3025 4299 4.194720 AGCCACGTCGATCTCGGC 62.195 66.667 0.00 9.37 43.31 5.54
3026 4300 2.024871 GAGCCACGTCGATCTCGG 59.975 66.667 0.00 0.00 40.29 4.63
3027 4301 2.351322 CGAGCCACGTCGATCTCG 60.351 66.667 16.13 16.13 42.85 4.04
3037 4311 2.476051 CAACATCGCACGAGCCAC 59.524 61.111 0.00 0.00 37.52 5.01
3038 4312 2.741985 CCAACATCGCACGAGCCA 60.742 61.111 0.00 0.00 37.52 4.75
3039 4313 3.499737 CCCAACATCGCACGAGCC 61.500 66.667 0.00 0.00 37.52 4.70
3040 4314 4.166011 GCCCAACATCGCACGAGC 62.166 66.667 0.00 0.00 37.42 5.03
3041 4315 2.434884 AGCCCAACATCGCACGAG 60.435 61.111 0.00 0.00 0.00 4.18
3042 4316 2.434185 GAGCCCAACATCGCACGA 60.434 61.111 0.00 0.00 0.00 4.35
3043 4317 3.499737 GGAGCCCAACATCGCACG 61.500 66.667 0.00 0.00 0.00 5.34
3044 4318 1.648467 GAAGGAGCCCAACATCGCAC 61.648 60.000 0.00 0.00 0.00 5.34
3045 4319 1.377202 GAAGGAGCCCAACATCGCA 60.377 57.895 0.00 0.00 0.00 5.10
3067 4341 0.538584 TGCAGTGTGGAGCTGGATAG 59.461 55.000 0.00 0.00 34.73 2.08
3068 4342 0.983467 TTGCAGTGTGGAGCTGGATA 59.017 50.000 0.00 0.00 34.41 2.59
3069 4343 0.111061 TTTGCAGTGTGGAGCTGGAT 59.889 50.000 0.00 0.00 34.41 3.41
3070 4344 0.535780 CTTTGCAGTGTGGAGCTGGA 60.536 55.000 0.00 0.00 34.73 3.86
3071 4345 1.954528 CTTTGCAGTGTGGAGCTGG 59.045 57.895 0.00 0.00 34.73 4.85
3072 4346 1.285023 GCTTTGCAGTGTGGAGCTG 59.715 57.895 0.00 0.00 37.06 4.24
3073 4347 1.152902 TGCTTTGCAGTGTGGAGCT 60.153 52.632 12.64 0.00 33.32 4.09
3074 4348 1.008079 GTGCTTTGCAGTGTGGAGC 60.008 57.895 6.76 6.76 40.08 4.70
3075 4349 0.029834 GTGTGCTTTGCAGTGTGGAG 59.970 55.000 0.00 0.00 40.08 3.86
3076 4350 1.713937 CGTGTGCTTTGCAGTGTGGA 61.714 55.000 0.00 0.00 40.08 4.02
3077 4351 1.298563 CGTGTGCTTTGCAGTGTGG 60.299 57.895 0.00 0.00 40.08 4.17
3078 4352 1.940758 GCGTGTGCTTTGCAGTGTG 60.941 57.895 0.00 0.00 40.08 3.82
3079 4353 2.408835 GCGTGTGCTTTGCAGTGT 59.591 55.556 0.00 0.00 40.08 3.55
3080 4354 2.353839 GGCGTGTGCTTTGCAGTG 60.354 61.111 0.00 0.00 40.08 3.66
3081 4355 3.952675 CGGCGTGTGCTTTGCAGT 61.953 61.111 0.00 0.00 40.08 4.40
3082 4356 4.688419 CCGGCGTGTGCTTTGCAG 62.688 66.667 6.01 0.00 40.08 4.41
3085 4359 4.688419 CAGCCGGCGTGTGCTTTG 62.688 66.667 23.20 7.30 42.25 2.77
3116 4390 0.385390 CTTGTTCCCCAACTGCACAC 59.615 55.000 0.00 0.00 33.17 3.82


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

AutoCloner maintained by Alex Coulton.