Multiple sequence alignment - TraesCS1A01G019400

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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 TraesCS1A01G019400 chr1A 100.000 4050 0 0 1 4050 9761052 9765101 0.000000e+00 7480.0
1 TraesCS1A01G019400 chr6B 93.942 3120 160 15 941 4050 30405474 30402374 0.000000e+00 4687.0
2 TraesCS1A01G019400 chr6B 83.945 2099 221 63 688 2733 31261940 31259905 0.000000e+00 1903.0
3 TraesCS1A01G019400 chr6B 85.558 1828 185 38 941 2733 30597117 30595334 0.000000e+00 1840.0
4 TraesCS1A01G019400 chr6B 84.356 1010 115 20 1266 2255 30557852 30556866 0.000000e+00 950.0
5 TraesCS1A01G019400 chr6B 84.916 895 100 23 2874 3754 31259913 31259040 0.000000e+00 872.0
6 TraesCS1A01G019400 chr6B 84.487 896 103 23 2874 3754 30595342 30594468 0.000000e+00 852.0
7 TraesCS1A01G019400 chr6B 83.911 895 109 23 2874 3754 30556050 30555177 0.000000e+00 822.0
8 TraesCS1A01G019400 chr6B 84.293 764 96 13 1981 2733 30556792 30556042 0.000000e+00 725.0
9 TraesCS1A01G019400 chr6B 94.737 209 8 3 941 1149 30558567 30558362 5.050000e-84 322.0
10 TraesCS1A01G019400 chr6B 89.100 211 9 4 649 855 30558923 30558723 2.420000e-62 250.0
11 TraesCS1A01G019400 chr6B 88.506 174 8 3 684 855 30597436 30597273 2.470000e-47 200.0
12 TraesCS1A01G019400 chr6B 91.860 86 6 1 9 93 19451287 19451202 7.110000e-23 119.0
13 TraesCS1A01G019400 chr6A 93.649 1795 101 5 941 2733 18356057 18354274 0.000000e+00 2671.0
14 TraesCS1A01G019400 chr6A 83.333 1122 130 31 2874 3981 18354282 18353204 0.000000e+00 983.0
15 TraesCS1A01G019400 chr6D 88.841 2106 163 34 683 2733 17791188 17793276 0.000000e+00 2521.0
16 TraesCS1A01G019400 chr6D 91.005 1801 133 8 949 2733 17470562 17468775 0.000000e+00 2401.0
17 TraesCS1A01G019400 chr6D 84.676 894 97 25 2874 3750 17793268 17794138 0.000000e+00 856.0
18 TraesCS1A01G019400 chr6D 83.176 850 108 11 1296 2143 17449055 17448239 0.000000e+00 745.0
19 TraesCS1A01G019400 chr6D 84.944 538 61 12 106 630 90442874 90442344 9.970000e-146 527.0
20 TraesCS1A01G019400 chr6D 85.401 411 46 8 2874 3280 17468783 17468383 8.100000e-112 414.0
21 TraesCS1A01G019400 chr6D 88.197 305 24 6 969 1273 17449248 17448956 1.790000e-93 353.0
22 TraesCS1A01G019400 chr6D 81.553 206 32 3 2134 2338 17447039 17446839 9.010000e-37 165.0
23 TraesCS1A01G019400 chr6D 78.788 165 33 2 1433 1596 3823333 3823170 4.280000e-20 110.0
24 TraesCS1A01G019400 chr3D 86.826 501 61 4 106 606 74327409 74326914 4.570000e-154 555.0
25 TraesCS1A01G019400 chr3D 86.761 423 51 5 223 645 178404385 178403968 2.200000e-127 466.0
26 TraesCS1A01G019400 chr3D 93.939 99 6 0 2776 2874 536919732 536919634 2.520000e-32 150.0
27 TraesCS1A01G019400 chr2A 88.180 423 47 3 202 624 16710636 16711055 6.040000e-138 501.0
28 TraesCS1A01G019400 chr2A 91.018 167 13 1 106 272 16710454 16710618 1.460000e-54 224.0
29 TraesCS1A01G019400 chr2A 80.385 260 43 6 109 365 58171876 58171622 1.490000e-44 191.0
30 TraesCS1A01G019400 chr2A 91.667 108 9 0 2776 2883 11897784 11897891 2.520000e-32 150.0
31 TraesCS1A01G019400 chr5B 82.752 545 73 12 106 638 373663854 373663319 2.200000e-127 466.0
32 TraesCS1A01G019400 chrUn 82.385 545 77 9 106 638 331240576 331241113 1.330000e-124 457.0
33 TraesCS1A01G019400 chrUn 89.815 108 10 1 2776 2882 300566630 300566523 1.960000e-28 137.0
34 TraesCS1A01G019400 chrUn 89.815 108 10 1 2776 2882 353964286 353964393 1.960000e-28 137.0
35 TraesCS1A01G019400 chrUn 91.358 81 7 0 9 89 338055772 338055852 1.190000e-20 111.0
36 TraesCS1A01G019400 chrUn 88.298 94 10 1 1 93 385850129 385850036 1.190000e-20 111.0
37 TraesCS1A01G019400 chrUn 93.333 45 2 1 2994 3037 51909479 51909523 9.400000e-07 65.8
38 TraesCS1A01G019400 chr3B 86.461 421 52 5 220 638 267223377 267223794 1.330000e-124 457.0
39 TraesCS1A01G019400 chr3B 92.079 101 8 0 2776 2876 177086459 177086359 4.220000e-30 143.0
40 TraesCS1A01G019400 chr3B 94.118 51 3 0 10 60 572865462 572865512 1.210000e-10 78.7
41 TraesCS1A01G019400 chr1B 82.018 545 77 10 106 638 6262624 6263159 1.030000e-120 444.0
42 TraesCS1A01G019400 chr7A 85.253 434 56 7 220 651 374007806 374007379 1.340000e-119 440.0
43 TraesCS1A01G019400 chr2D 93.137 102 7 0 2775 2876 639533793 639533692 2.520000e-32 150.0
44 TraesCS1A01G019400 chr7D 93.878 98 6 0 2776 2873 464028845 464028942 9.070000e-32 148.0
45 TraesCS1A01G019400 chr3A 90.476 105 10 0 2776 2880 710791166 710791062 5.460000e-29 139.0
46 TraesCS1A01G019400 chr4D 81.410 156 25 3 1017 1169 490413412 490413258 1.530000e-24 124.0
47 TraesCS1A01G019400 chr4D 92.105 76 5 1 6 80 380341159 380341234 5.540000e-19 106.0
48 TraesCS1A01G019400 chr7B 92.405 79 6 0 9 87 721315112 721315034 3.310000e-21 113.0
49 TraesCS1A01G019400 chr4B 79.381 97 17 3 2944 3037 2693220 2693316 9.400000e-07 65.8


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 TraesCS1A01G019400 chr1A 9761052 9765101 4049 False 7480.0 7480 100.000000 1 4050 1 chr1A.!!$F1 4049
1 TraesCS1A01G019400 chr6B 30402374 30405474 3100 True 4687.0 4687 93.942000 941 4050 1 chr6B.!!$R2 3109
2 TraesCS1A01G019400 chr6B 31259040 31261940 2900 True 1387.5 1903 84.430500 688 3754 2 chr6B.!!$R5 3066
3 TraesCS1A01G019400 chr6B 30594468 30597436 2968 True 964.0 1840 86.183667 684 3754 3 chr6B.!!$R4 3070
4 TraesCS1A01G019400 chr6B 30555177 30558923 3746 True 613.8 950 87.279400 649 3754 5 chr6B.!!$R3 3105
5 TraesCS1A01G019400 chr6A 18353204 18356057 2853 True 1827.0 2671 88.491000 941 3981 2 chr6A.!!$R1 3040
6 TraesCS1A01G019400 chr6D 17791188 17794138 2950 False 1688.5 2521 86.758500 683 3750 2 chr6D.!!$F1 3067
7 TraesCS1A01G019400 chr6D 17468383 17470562 2179 True 1407.5 2401 88.203000 949 3280 2 chr6D.!!$R4 2331
8 TraesCS1A01G019400 chr6D 90442344 90442874 530 True 527.0 527 84.944000 106 630 1 chr6D.!!$R2 524
9 TraesCS1A01G019400 chr6D 17446839 17449248 2409 True 421.0 745 84.308667 969 2338 3 chr6D.!!$R3 1369
10 TraesCS1A01G019400 chr2A 16710454 16711055 601 False 362.5 501 89.599000 106 624 2 chr2A.!!$F2 518
11 TraesCS1A01G019400 chr5B 373663319 373663854 535 True 466.0 466 82.752000 106 638 1 chr5B.!!$R1 532
12 TraesCS1A01G019400 chrUn 331240576 331241113 537 False 457.0 457 82.385000 106 638 1 chrUn.!!$F2 532
13 TraesCS1A01G019400 chr1B 6262624 6263159 535 False 444.0 444 82.018000 106 638 1 chr1B.!!$F1 532

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
32 33 0.396556 GAGAGGTGGGAGAGGGAGTC 60.397 65.000 0.00 0.0 0.0 3.36 F
1543 2150 0.034896 TTTTCCACCAGAGCTCCGTC 59.965 55.000 10.93 0.0 0.0 4.79 F
1944 2565 0.180406 ACGACAGTGTTCTTGGCCTT 59.820 50.000 3.32 0.0 0.0 4.35 F
2790 5183 1.001860 TCACATGAGCCGTTGATGTCA 59.998 47.619 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2460 0.179134 CTCGATGACACGAAGGGTCC 60.179 60.000 0.00 0.00 41.67 4.46 R
2836 5229 0.198696 TCCCTCTTTCCCCCTCCTTT 59.801 55.000 0.00 0.00 0.00 3.11 R
2837 5230 0.253394 CTCCCTCTTTCCCCCTCCTT 60.253 60.000 0.00 0.00 0.00 3.36 R
3766 6191 1.147817 AGTTCACTTGGCCAGGGATTT 59.852 47.619 20.34 3.09 33.65 2.17 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
17 18 2.183811 CGACAGCAGGCAGGAGAG 59.816 66.667 0.00 0.00 0.00 3.20
18 19 2.583520 GACAGCAGGCAGGAGAGG 59.416 66.667 0.00 0.00 0.00 3.69
19 20 2.203907 ACAGCAGGCAGGAGAGGT 60.204 61.111 0.00 0.00 0.00 3.85
20 21 2.268280 CAGCAGGCAGGAGAGGTG 59.732 66.667 0.00 0.00 0.00 4.00
21 22 3.007920 AGCAGGCAGGAGAGGTGG 61.008 66.667 0.00 0.00 0.00 4.61
22 23 4.106925 GCAGGCAGGAGAGGTGGG 62.107 72.222 0.00 0.00 0.00 4.61
23 24 2.284921 CAGGCAGGAGAGGTGGGA 60.285 66.667 0.00 0.00 0.00 4.37
24 25 2.040278 AGGCAGGAGAGGTGGGAG 59.960 66.667 0.00 0.00 0.00 4.30
25 26 2.039624 GGCAGGAGAGGTGGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
26 27 2.063378 GGCAGGAGAGGTGGGAGAG 61.063 68.421 0.00 0.00 0.00 3.20
27 28 2.063378 GCAGGAGAGGTGGGAGAGG 61.063 68.421 0.00 0.00 0.00 3.69
28 29 1.382420 CAGGAGAGGTGGGAGAGGG 60.382 68.421 0.00 0.00 0.00 4.30
29 30 1.547755 AGGAGAGGTGGGAGAGGGA 60.548 63.158 0.00 0.00 0.00 4.20
30 31 1.075600 GGAGAGGTGGGAGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
31 32 1.700985 GAGAGGTGGGAGAGGGAGT 59.299 63.158 0.00 0.00 0.00 3.85
32 33 0.396556 GAGAGGTGGGAGAGGGAGTC 60.397 65.000 0.00 0.00 0.00 3.36
33 34 1.755008 GAGGTGGGAGAGGGAGTCG 60.755 68.421 0.00 0.00 0.00 4.18
34 35 2.212794 GAGGTGGGAGAGGGAGTCGA 62.213 65.000 0.00 0.00 0.00 4.20
35 36 1.755008 GGTGGGAGAGGGAGTCGAG 60.755 68.421 0.00 0.00 0.00 4.04
36 37 1.755008 GTGGGAGAGGGAGTCGAGG 60.755 68.421 0.00 0.00 0.00 4.63
37 38 2.123640 GGGAGAGGGAGTCGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
38 39 2.835895 GGAGAGGGAGTCGAGGGC 60.836 72.222 0.00 0.00 0.00 5.19
39 40 2.277404 GAGAGGGAGTCGAGGGCT 59.723 66.667 0.00 0.00 0.00 5.19
40 41 2.043450 AGAGGGAGTCGAGGGCTG 60.043 66.667 0.00 0.00 0.00 4.85
41 42 3.151022 GAGGGAGTCGAGGGCTGG 61.151 72.222 0.00 0.00 0.00 4.85
42 43 4.787280 AGGGAGTCGAGGGCTGGG 62.787 72.222 0.00 0.00 0.00 4.45
44 45 3.775654 GGAGTCGAGGGCTGGGTG 61.776 72.222 0.00 0.00 0.00 4.61
45 46 3.775654 GAGTCGAGGGCTGGGTGG 61.776 72.222 0.00 0.00 0.00 4.61
55 56 3.717294 CTGGGTGGCGCTAGGGTT 61.717 66.667 7.64 0.00 0.00 4.11
56 57 3.682292 CTGGGTGGCGCTAGGGTTC 62.682 68.421 7.64 2.35 0.00 3.62
57 58 4.484872 GGGTGGCGCTAGGGTTCC 62.485 72.222 7.64 0.00 0.00 3.62
58 59 4.484872 GGTGGCGCTAGGGTTCCC 62.485 72.222 7.64 0.00 0.00 3.97
59 60 4.484872 GTGGCGCTAGGGTTCCCC 62.485 72.222 7.64 1.60 45.90 4.81
69 70 4.410400 GGTTCCCCCTGGTCGCTG 62.410 72.222 0.00 0.00 0.00 5.18
95 96 3.077556 CGTCCCAGGGGTGAGGAG 61.078 72.222 5.33 0.00 36.47 3.69
96 97 2.689034 GTCCCAGGGGTGAGGAGG 60.689 72.222 5.33 0.00 36.47 4.30
97 98 4.024984 TCCCAGGGGTGAGGAGGG 62.025 72.222 5.33 0.00 36.47 4.30
99 100 4.024984 CCAGGGGTGAGGAGGGGA 62.025 72.222 0.00 0.00 0.00 4.81
100 101 2.366167 CAGGGGTGAGGAGGGGAG 60.366 72.222 0.00 0.00 0.00 4.30
101 102 2.540910 AGGGGTGAGGAGGGGAGA 60.541 66.667 0.00 0.00 0.00 3.71
102 103 2.041405 GGGGTGAGGAGGGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
103 104 2.781406 GGGTGAGGAGGGGAGAGT 59.219 66.667 0.00 0.00 0.00 3.24
104 105 1.591280 GGGGTGAGGAGGGGAGAGTA 61.591 65.000 0.00 0.00 0.00 2.59
122 123 9.281371 GGGAGAGTAAAATGTAGTTGTAAAAGT 57.719 33.333 0.00 0.00 0.00 2.66
150 151 6.177610 ACAACTCTCTCTGTTTTGGTTAACA 58.822 36.000 8.10 0.00 36.63 2.41
162 163 7.085116 TGTTTTGGTTAACAATATAGTTGCCG 58.915 34.615 8.10 0.00 39.21 5.69
213 225 4.989279 ATCAAACCATAGTTGTCATGCC 57.011 40.909 0.00 0.00 35.97 4.40
272 372 4.069304 GCCATGTGTGTTTACCTAGTTGA 58.931 43.478 0.00 0.00 0.00 3.18
278 378 4.026310 GTGTGTTTACCTAGTTGACACGTG 60.026 45.833 15.48 15.48 42.53 4.49
308 408 5.994250 ACTGCAGTTGTCATATCTACCAAT 58.006 37.500 15.25 0.00 0.00 3.16
346 446 1.071071 TGTGTTTACCTAGTTGCCGCT 59.929 47.619 0.00 0.00 0.00 5.52
376 476 2.634940 ACTGCAGTTGTCATCTACCACT 59.365 45.455 15.25 0.00 34.50 4.00
442 543 1.408266 GGAGTGGTTGGTGACTGTGTT 60.408 52.381 0.00 0.00 0.00 3.32
444 545 1.280710 AGTGGTTGGTGACTGTGTTGA 59.719 47.619 0.00 0.00 0.00 3.18
529 630 1.808411 CTCTAACGCCCACACAACAT 58.192 50.000 0.00 0.00 0.00 2.71
538 639 2.435422 CCCACACAACATGCTATGTCA 58.565 47.619 0.00 0.00 44.07 3.58
543 644 4.151512 CACACAACATGCTATGTCAACGTA 59.848 41.667 0.00 0.00 44.07 3.57
567 678 5.190528 AGCACTCAGATTCCTTTAGGATTCA 59.809 40.000 18.12 0.00 44.98 2.57
577 688 6.662865 TCCTTTAGGATTCATGCAAAACAA 57.337 33.333 0.00 0.00 39.78 2.83
640 751 1.986698 ACACGTGTGAGCGTTATACC 58.013 50.000 22.71 0.00 43.83 2.73
641 752 1.270274 ACACGTGTGAGCGTTATACCA 59.730 47.619 22.71 0.00 43.83 3.25
642 753 2.094390 ACACGTGTGAGCGTTATACCAT 60.094 45.455 22.71 0.00 43.83 3.55
643 754 2.927477 CACGTGTGAGCGTTATACCATT 59.073 45.455 7.58 0.00 43.83 3.16
644 755 3.369756 CACGTGTGAGCGTTATACCATTT 59.630 43.478 7.58 0.00 43.83 2.32
645 756 4.563580 CACGTGTGAGCGTTATACCATTTA 59.436 41.667 7.58 0.00 43.83 1.40
646 757 4.802039 ACGTGTGAGCGTTATACCATTTAG 59.198 41.667 0.00 0.00 43.04 1.85
647 758 5.038683 CGTGTGAGCGTTATACCATTTAGA 58.961 41.667 0.00 0.00 0.00 2.10
781 896 4.689345 CGGAATCGAAACTAACTTGTCCTT 59.311 41.667 0.00 0.00 39.00 3.36
782 897 5.865552 CGGAATCGAAACTAACTTGTCCTTA 59.134 40.000 0.00 0.00 39.00 2.69
837 952 1.726853 GGACACGGAGTTCCAATCTG 58.273 55.000 0.00 0.00 41.61 2.90
856 971 6.604735 ATCTGACCGCAAAGTTCATATAAC 57.395 37.500 0.00 0.00 0.00 1.89
857 972 5.483811 TCTGACCGCAAAGTTCATATAACA 58.516 37.500 0.00 0.00 0.00 2.41
879 1029 3.155167 GTCCCGCTTCCCGATCCT 61.155 66.667 0.00 0.00 40.02 3.24
882 1032 4.286320 CCGCTTCCCGATCCTCCG 62.286 72.222 0.00 0.00 40.02 4.63
883 1033 3.217017 CGCTTCCCGATCCTCCGA 61.217 66.667 0.00 0.00 40.02 4.55
884 1034 2.417936 GCTTCCCGATCCTCCGAC 59.582 66.667 0.00 0.00 0.00 4.79
885 1035 2.722487 CTTCCCGATCCTCCGACG 59.278 66.667 0.00 0.00 0.00 5.12
886 1036 3.486252 CTTCCCGATCCTCCGACGC 62.486 68.421 0.00 0.00 0.00 5.19
941 1092 3.103911 GTGTCGCACGGTTCCTCG 61.104 66.667 0.00 0.00 0.00 4.63
966 1158 2.589159 GGCTAGCTACTTGCCGGC 60.589 66.667 22.73 22.73 41.74 6.13
1009 1201 2.181525 GCCGCGCCATGTCAATTT 59.818 55.556 0.00 0.00 0.00 1.82
1227 1419 0.181350 ATTCCGCCTTCACTCCCATC 59.819 55.000 0.00 0.00 0.00 3.51
1228 1420 0.909610 TTCCGCCTTCACTCCCATCT 60.910 55.000 0.00 0.00 0.00 2.90
1229 1421 0.909610 TCCGCCTTCACTCCCATCTT 60.910 55.000 0.00 0.00 0.00 2.40
1230 1422 0.745845 CCGCCTTCACTCCCATCTTG 60.746 60.000 0.00 0.00 0.00 3.02
1231 1423 0.745845 CGCCTTCACTCCCATCTTGG 60.746 60.000 0.00 0.00 37.25 3.61
1232 1424 0.620556 GCCTTCACTCCCATCTTGGA 59.379 55.000 0.00 0.00 40.96 3.53
1290 1875 4.509616 TCTTTGTTCGGTTTCTTCACAGA 58.490 39.130 0.00 0.00 0.00 3.41
1334 1934 2.554462 GTTTCTCCAAAGGGTCTCTTGC 59.446 50.000 0.00 0.00 35.55 4.01
1342 1942 1.439543 AGGGTCTCTTGCCTTCACTT 58.560 50.000 0.00 0.00 0.00 3.16
1430 2037 0.106419 GGGGCGGATTGGGAATTACA 60.106 55.000 0.00 0.00 0.00 2.41
1543 2150 0.034896 TTTTCCACCAGAGCTCCGTC 59.965 55.000 10.93 0.00 0.00 4.79
1625 2238 0.395586 GGGCATGTGCACCAGGATTA 60.396 55.000 15.69 0.00 44.36 1.75
1707 2320 4.811024 TCATTCGCTTGTGTCTATGATTCC 59.189 41.667 0.00 0.00 0.00 3.01
1724 2337 2.725641 CGCGTCGGATGTATGGGA 59.274 61.111 0.00 0.00 0.00 4.37
1840 2453 5.277297 CGCGAAATCCTTGCATTTGATACTA 60.277 40.000 0.00 0.00 0.00 1.82
1847 2460 5.036737 CCTTGCATTTGATACTAAAAGGCG 58.963 41.667 0.00 0.00 44.85 5.52
1929 2550 1.331138 CTCCTACGGACAGATGACGAC 59.669 57.143 8.24 0.00 0.00 4.34
1944 2565 0.180406 ACGACAGTGTTCTTGGCCTT 59.820 50.000 3.32 0.00 0.00 4.35
1970 2609 4.089105 GTCCAAACCGGGCATTCA 57.911 55.556 6.32 0.00 40.18 2.57
1971 2610 2.578683 GTCCAAACCGGGCATTCAT 58.421 52.632 6.32 0.00 40.18 2.57
1972 2611 1.757682 GTCCAAACCGGGCATTCATA 58.242 50.000 6.32 0.00 40.18 2.15
1973 2612 2.306847 GTCCAAACCGGGCATTCATAT 58.693 47.619 6.32 0.00 40.18 1.78
1974 2613 3.482436 GTCCAAACCGGGCATTCATATA 58.518 45.455 6.32 0.00 40.18 0.86
1975 2614 4.079253 GTCCAAACCGGGCATTCATATAT 58.921 43.478 6.32 0.00 40.18 0.86
1976 2615 4.078537 TCCAAACCGGGCATTCATATATG 58.921 43.478 6.32 6.36 34.36 1.78
1977 2616 3.193267 CCAAACCGGGCATTCATATATGG 59.807 47.826 12.78 0.00 0.00 2.74
1978 2617 2.806945 ACCGGGCATTCATATATGGG 57.193 50.000 12.78 6.62 0.00 4.00
1979 2618 2.274542 ACCGGGCATTCATATATGGGA 58.725 47.619 12.78 2.84 0.00 4.37
1980 2619 2.239654 ACCGGGCATTCATATATGGGAG 59.760 50.000 12.78 4.23 0.00 4.30
1981 2620 2.421952 CCGGGCATTCATATATGGGAGG 60.422 54.545 12.78 5.30 0.00 4.30
1982 2621 2.421952 CGGGCATTCATATATGGGAGGG 60.422 54.545 12.78 0.64 0.00 4.30
1983 2622 2.659428 GGCATTCATATATGGGAGGGC 58.341 52.381 12.78 11.50 0.00 5.19
1984 2623 2.025037 GGCATTCATATATGGGAGGGCA 60.025 50.000 12.78 0.00 0.00 5.36
1985 2624 3.373438 GGCATTCATATATGGGAGGGCAT 60.373 47.826 12.78 0.00 0.00 4.40
1986 2625 4.284178 GCATTCATATATGGGAGGGCATT 58.716 43.478 12.78 0.00 0.00 3.56
1987 2626 4.340381 GCATTCATATATGGGAGGGCATTC 59.660 45.833 12.78 0.00 0.00 2.67
2035 2692 2.438434 GTCTTGCCGGATGGGTGG 60.438 66.667 5.05 0.00 38.44 4.61
2082 2739 1.135286 GGGATCTTTTCTTGCGCCTTG 60.135 52.381 4.18 0.00 0.00 3.61
2184 4050 3.449018 ACCTTAAGTCGATGCAGATCAGT 59.551 43.478 0.97 0.00 0.00 3.41
2193 4059 6.595326 AGTCGATGCAGATCAGTTTAATTTCA 59.405 34.615 0.00 0.00 0.00 2.69
2208 4422 7.863877 AGTTTAATTTCAAAACCGAATAAGCGT 59.136 29.630 0.00 0.00 37.51 5.07
2527 4768 3.427503 GGTGGCATGTACTTTTTCATCGG 60.428 47.826 0.00 0.00 0.00 4.18
2530 4772 4.520874 TGGCATGTACTTTTTCATCGGAAA 59.479 37.500 0.00 0.00 41.13 3.13
2619 4864 6.994496 TCCCAATTTGTGCATATTTTGTTTGA 59.006 30.769 0.00 0.00 0.00 2.69
2658 4903 6.599356 TTAACAGGTACATAGTCTCTGCAA 57.401 37.500 0.00 0.00 0.00 4.08
2717 4962 4.021102 AGTAGTCCAAACATGTCTTGGG 57.979 45.455 26.04 15.30 43.10 4.12
2736 5129 9.004717 GTCTTGGGAAAGGAATATTATAAGAGC 57.995 37.037 0.00 0.00 0.00 4.09
2737 5130 8.723365 TCTTGGGAAAGGAATATTATAAGAGCA 58.277 33.333 0.00 0.00 0.00 4.26
2738 5131 8.924511 TTGGGAAAGGAATATTATAAGAGCAG 57.075 34.615 0.00 0.00 0.00 4.24
2739 5132 8.045720 TGGGAAAGGAATATTATAAGAGCAGT 57.954 34.615 0.00 0.00 0.00 4.40
2740 5133 8.502738 TGGGAAAGGAATATTATAAGAGCAGTT 58.497 33.333 0.00 0.00 0.00 3.16
2741 5134 9.355916 GGGAAAGGAATATTATAAGAGCAGTTT 57.644 33.333 0.00 0.00 0.00 2.66
2760 5153 7.410485 GCAGTTTTAATATGCTCACTCTTACC 58.590 38.462 0.00 0.00 37.00 2.85
2761 5154 7.467403 GCAGTTTTAATATGCTCACTCTTACCC 60.467 40.741 0.00 0.00 37.00 3.69
2762 5155 7.012421 CAGTTTTAATATGCTCACTCTTACCCC 59.988 40.741 0.00 0.00 0.00 4.95
2763 5156 5.562298 TTAATATGCTCACTCTTACCCCC 57.438 43.478 0.00 0.00 0.00 5.40
2779 5172 1.467920 CCCCCTCTTTTCACATGAGC 58.532 55.000 0.00 0.00 0.00 4.26
2780 5173 1.467920 CCCCTCTTTTCACATGAGCC 58.532 55.000 0.00 0.00 0.00 4.70
2781 5174 1.089920 CCCTCTTTTCACATGAGCCG 58.910 55.000 0.00 0.00 0.00 5.52
2782 5175 1.611673 CCCTCTTTTCACATGAGCCGT 60.612 52.381 0.00 0.00 0.00 5.68
2783 5176 2.154462 CCTCTTTTCACATGAGCCGTT 58.846 47.619 0.00 0.00 0.00 4.44
2784 5177 2.095567 CCTCTTTTCACATGAGCCGTTG 60.096 50.000 0.00 0.00 0.00 4.10
2785 5178 2.807967 CTCTTTTCACATGAGCCGTTGA 59.192 45.455 0.00 0.00 0.00 3.18
2786 5179 3.411446 TCTTTTCACATGAGCCGTTGAT 58.589 40.909 0.00 0.00 0.00 2.57
2787 5180 3.189080 TCTTTTCACATGAGCCGTTGATG 59.811 43.478 0.00 0.00 0.00 3.07
2788 5181 2.183478 TTCACATGAGCCGTTGATGT 57.817 45.000 0.00 0.00 0.00 3.06
2789 5182 1.725641 TCACATGAGCCGTTGATGTC 58.274 50.000 0.00 0.00 0.00 3.06
2790 5183 1.001860 TCACATGAGCCGTTGATGTCA 59.998 47.619 0.00 0.00 0.00 3.58
2791 5184 2.011947 CACATGAGCCGTTGATGTCAT 58.988 47.619 0.00 0.00 0.00 3.06
2792 5185 2.421073 CACATGAGCCGTTGATGTCATT 59.579 45.455 0.00 0.00 0.00 2.57
2793 5186 3.622612 CACATGAGCCGTTGATGTCATTA 59.377 43.478 0.00 0.00 0.00 1.90
2794 5187 4.094739 CACATGAGCCGTTGATGTCATTAA 59.905 41.667 0.00 0.00 0.00 1.40
2795 5188 4.883585 ACATGAGCCGTTGATGTCATTAAT 59.116 37.500 0.00 0.00 0.00 1.40
2796 5189 5.357878 ACATGAGCCGTTGATGTCATTAATT 59.642 36.000 0.00 0.00 0.00 1.40
2797 5190 6.542005 ACATGAGCCGTTGATGTCATTAATTA 59.458 34.615 0.00 0.00 0.00 1.40
2798 5191 6.603237 TGAGCCGTTGATGTCATTAATTAG 57.397 37.500 0.00 0.00 0.00 1.73
2799 5192 6.112734 TGAGCCGTTGATGTCATTAATTAGT 58.887 36.000 0.00 0.00 0.00 2.24
2800 5193 6.037062 TGAGCCGTTGATGTCATTAATTAGTG 59.963 38.462 1.66 1.66 0.00 2.74
2801 5194 6.112734 AGCCGTTGATGTCATTAATTAGTGA 58.887 36.000 6.58 6.58 0.00 3.41
2802 5195 6.767902 AGCCGTTGATGTCATTAATTAGTGAT 59.232 34.615 13.12 0.00 0.00 3.06
2803 5196 7.931407 AGCCGTTGATGTCATTAATTAGTGATA 59.069 33.333 13.12 11.16 0.00 2.15
2804 5197 8.721478 GCCGTTGATGTCATTAATTAGTGATAT 58.279 33.333 16.62 16.62 0.00 1.63
2829 5222 8.660295 TGATTAACTCTTACCTTCTTACCTCA 57.340 34.615 0.00 0.00 0.00 3.86
2830 5223 8.529476 TGATTAACTCTTACCTTCTTACCTCAC 58.471 37.037 0.00 0.00 0.00 3.51
2831 5224 7.844493 TTAACTCTTACCTTCTTACCTCACA 57.156 36.000 0.00 0.00 0.00 3.58
2832 5225 6.936968 AACTCTTACCTTCTTACCTCACAT 57.063 37.500 0.00 0.00 0.00 3.21
2833 5226 6.287589 ACTCTTACCTTCTTACCTCACATG 57.712 41.667 0.00 0.00 0.00 3.21
2834 5227 5.780793 ACTCTTACCTTCTTACCTCACATGT 59.219 40.000 0.00 0.00 0.00 3.21
2835 5228 6.952358 ACTCTTACCTTCTTACCTCACATGTA 59.048 38.462 0.00 0.00 0.00 2.29
2836 5229 7.453752 ACTCTTACCTTCTTACCTCACATGTAA 59.546 37.037 0.00 0.00 0.00 2.41
2837 5230 8.197592 TCTTACCTTCTTACCTCACATGTAAA 57.802 34.615 0.00 0.00 0.00 2.01
2838 5231 8.653191 TCTTACCTTCTTACCTCACATGTAAAA 58.347 33.333 0.00 0.00 0.00 1.52
2839 5232 8.842358 TTACCTTCTTACCTCACATGTAAAAG 57.158 34.615 0.00 0.00 0.00 2.27
2840 5233 6.238648 ACCTTCTTACCTCACATGTAAAAGG 58.761 40.000 15.91 15.91 39.34 3.11
2841 5234 6.043938 ACCTTCTTACCTCACATGTAAAAGGA 59.956 38.462 21.69 5.57 37.89 3.36
2842 5235 6.595716 CCTTCTTACCTCACATGTAAAAGGAG 59.404 42.308 21.69 13.53 37.89 3.69
2845 5238 3.004752 CCTCACATGTAAAAGGAGGGG 57.995 52.381 17.52 1.94 41.12 4.79
2846 5239 2.357154 CCTCACATGTAAAAGGAGGGGG 60.357 54.545 17.52 1.25 41.12 5.40
2847 5240 2.576191 CTCACATGTAAAAGGAGGGGGA 59.424 50.000 0.00 0.00 0.00 4.81
2848 5241 2.990284 TCACATGTAAAAGGAGGGGGAA 59.010 45.455 0.00 0.00 0.00 3.97
2849 5242 3.399644 TCACATGTAAAAGGAGGGGGAAA 59.600 43.478 0.00 0.00 0.00 3.13
2850 5243 3.763897 CACATGTAAAAGGAGGGGGAAAG 59.236 47.826 0.00 0.00 0.00 2.62
2851 5244 3.660669 ACATGTAAAAGGAGGGGGAAAGA 59.339 43.478 0.00 0.00 0.00 2.52
2852 5245 4.263949 ACATGTAAAAGGAGGGGGAAAGAG 60.264 45.833 0.00 0.00 0.00 2.85
2853 5246 2.647802 TGTAAAAGGAGGGGGAAAGAGG 59.352 50.000 0.00 0.00 0.00 3.69
2854 5247 1.084866 AAAAGGAGGGGGAAAGAGGG 58.915 55.000 0.00 0.00 0.00 4.30
2855 5248 0.198696 AAAGGAGGGGGAAAGAGGGA 59.801 55.000 0.00 0.00 0.00 4.20
2856 5249 0.253394 AAGGAGGGGGAAAGAGGGAG 60.253 60.000 0.00 0.00 0.00 4.30
2857 5250 2.379459 GGAGGGGGAAAGAGGGAGC 61.379 68.421 0.00 0.00 0.00 4.70
2858 5251 1.616628 GAGGGGGAAAGAGGGAGCA 60.617 63.158 0.00 0.00 0.00 4.26
2859 5252 0.990818 GAGGGGGAAAGAGGGAGCAT 60.991 60.000 0.00 0.00 0.00 3.79
2860 5253 1.228510 GGGGGAAAGAGGGAGCATG 59.771 63.158 0.00 0.00 0.00 4.06
2861 5254 1.575447 GGGGGAAAGAGGGAGCATGT 61.575 60.000 0.00 0.00 0.00 3.21
2862 5255 0.332972 GGGGAAAGAGGGAGCATGTT 59.667 55.000 0.00 0.00 0.00 2.71
2863 5256 1.564348 GGGGAAAGAGGGAGCATGTTA 59.436 52.381 0.00 0.00 0.00 2.41
2864 5257 2.025321 GGGGAAAGAGGGAGCATGTTAA 60.025 50.000 0.00 0.00 0.00 2.01
2865 5258 3.563479 GGGGAAAGAGGGAGCATGTTAAA 60.563 47.826 0.00 0.00 0.00 1.52
2866 5259 4.086457 GGGAAAGAGGGAGCATGTTAAAA 58.914 43.478 0.00 0.00 0.00 1.52
2867 5260 4.711846 GGGAAAGAGGGAGCATGTTAAAAT 59.288 41.667 0.00 0.00 0.00 1.82
2868 5261 5.187772 GGGAAAGAGGGAGCATGTTAAAATT 59.812 40.000 0.00 0.00 0.00 1.82
2869 5262 6.295859 GGGAAAGAGGGAGCATGTTAAAATTT 60.296 38.462 0.00 0.00 0.00 1.82
2870 5263 6.591448 GGAAAGAGGGAGCATGTTAAAATTTG 59.409 38.462 0.00 0.00 0.00 2.32
2871 5264 5.077134 AGAGGGAGCATGTTAAAATTTGC 57.923 39.130 0.00 0.00 35.34 3.68
2872 5265 4.081476 AGAGGGAGCATGTTAAAATTTGCC 60.081 41.667 0.00 0.00 35.71 4.52
2873 5266 3.582208 AGGGAGCATGTTAAAATTTGCCA 59.418 39.130 0.00 0.00 35.71 4.92
2874 5267 4.225717 AGGGAGCATGTTAAAATTTGCCAT 59.774 37.500 0.00 0.00 35.71 4.40
2875 5268 5.424895 AGGGAGCATGTTAAAATTTGCCATA 59.575 36.000 0.00 0.00 35.71 2.74
2876 5269 6.100134 AGGGAGCATGTTAAAATTTGCCATAT 59.900 34.615 0.00 0.00 35.71 1.78
2877 5270 6.767423 GGGAGCATGTTAAAATTTGCCATATT 59.233 34.615 0.00 0.00 35.71 1.28
2878 5271 7.930865 GGGAGCATGTTAAAATTTGCCATATTA 59.069 33.333 0.00 0.00 35.71 0.98
2879 5272 9.492973 GGAGCATGTTAAAATTTGCCATATTAT 57.507 29.630 0.00 0.00 35.71 1.28
3044 5439 3.519107 GTGGAAATGGGTGGATCCAAATT 59.481 43.478 18.20 13.79 43.21 1.82
3255 5665 2.269940 AGGTGTGCCTTGGAGTTAGAT 58.730 47.619 0.00 0.00 44.18 1.98
3268 5678 6.621316 TGGAGTTAGATCGCTAGTTCTTAG 57.379 41.667 0.00 0.00 0.00 2.18
3288 5698 8.389779 TCTTAGCAACTTGTTCATGATTTGTA 57.610 30.769 0.00 0.00 0.00 2.41
3366 5776 0.453950 CATGTCGCACAAAGAGCTGC 60.454 55.000 0.00 0.00 0.00 5.25
3455 5867 3.004419 CGTTCTCCTGCGAATGGTATCTA 59.996 47.826 0.00 0.00 0.00 1.98
3480 5892 4.142116 CCTTGCAATCCAATATGCTGAACA 60.142 41.667 0.00 0.00 42.97 3.18
3507 5919 5.307976 CCCCTACTTCATGATGATCCAGTTA 59.692 44.000 15.03 0.00 0.00 2.24
3508 5920 6.183361 CCCCTACTTCATGATGATCCAGTTAA 60.183 42.308 15.03 0.00 0.00 2.01
3698 6113 3.008704 AGTGCCTTTTACACCGTATTCCT 59.991 43.478 0.00 0.00 38.87 3.36
3812 6237 1.115326 GCATTACAAGGGATGGGGCC 61.115 60.000 0.00 0.00 0.00 5.80
3876 6302 2.167662 CCTAAAAACCGAACATGGCCT 58.832 47.619 3.32 0.00 0.00 5.19
3897 6323 6.239317 GGCCTGAGAAAACTTTAACTTTCCAT 60.239 38.462 0.00 0.00 32.94 3.41
3981 6407 5.591877 GCATCTACAACTGGGATTCTCAAAT 59.408 40.000 0.00 0.00 0.00 2.32
3995 6421 4.931661 TCTCAAATGACCCCTATACGTC 57.068 45.455 0.00 0.00 0.00 4.34
4021 6447 2.701073 CGGATAGTGACCGGTCATAC 57.299 55.000 38.11 26.39 45.65 2.39
4024 6450 2.225963 GGATAGTGACCGGTCATACTCG 59.774 54.545 38.11 0.00 42.18 4.18
4026 6452 0.809385 AGTGACCGGTCATACTCGTG 59.191 55.000 38.11 0.00 42.18 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.183811 CTCTCCTGCCTGCTGTCG 59.816 66.667 0.00 0.00 0.00 4.35
1 2 2.289532 ACCTCTCCTGCCTGCTGTC 61.290 63.158 0.00 0.00 0.00 3.51
3 4 2.268280 CACCTCTCCTGCCTGCTG 59.732 66.667 0.00 0.00 0.00 4.41
6 7 2.284921 TCCCACCTCTCCTGCCTG 60.285 66.667 0.00 0.00 0.00 4.85
8 9 2.039624 TCTCCCACCTCTCCTGCC 59.960 66.667 0.00 0.00 0.00 4.85
9 10 2.063378 CCTCTCCCACCTCTCCTGC 61.063 68.421 0.00 0.00 0.00 4.85
10 11 1.382420 CCCTCTCCCACCTCTCCTG 60.382 68.421 0.00 0.00 0.00 3.86
11 12 1.547755 TCCCTCTCCCACCTCTCCT 60.548 63.158 0.00 0.00 0.00 3.69
12 13 1.075600 CTCCCTCTCCCACCTCTCC 60.076 68.421 0.00 0.00 0.00 3.71
13 14 0.396556 GACTCCCTCTCCCACCTCTC 60.397 65.000 0.00 0.00 0.00 3.20
14 15 1.700985 GACTCCCTCTCCCACCTCT 59.299 63.158 0.00 0.00 0.00 3.69
15 16 1.755008 CGACTCCCTCTCCCACCTC 60.755 68.421 0.00 0.00 0.00 3.85
16 17 2.218115 CTCGACTCCCTCTCCCACCT 62.218 65.000 0.00 0.00 0.00 4.00
17 18 1.755008 CTCGACTCCCTCTCCCACC 60.755 68.421 0.00 0.00 0.00 4.61
18 19 1.755008 CCTCGACTCCCTCTCCCAC 60.755 68.421 0.00 0.00 0.00 4.61
19 20 2.684104 CCTCGACTCCCTCTCCCA 59.316 66.667 0.00 0.00 0.00 4.37
20 21 2.123640 CCCTCGACTCCCTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
21 22 2.835895 GCCCTCGACTCCCTCTCC 60.836 72.222 0.00 0.00 0.00 3.71
22 23 2.124693 CAGCCCTCGACTCCCTCTC 61.125 68.421 0.00 0.00 0.00 3.20
23 24 2.043450 CAGCCCTCGACTCCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
24 25 3.151022 CCAGCCCTCGACTCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
25 26 4.787280 CCCAGCCCTCGACTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
27 28 3.775654 CACCCAGCCCTCGACTCC 61.776 72.222 0.00 0.00 0.00 3.85
28 29 3.775654 CCACCCAGCCCTCGACTC 61.776 72.222 0.00 0.00 0.00 3.36
38 39 3.682292 GAACCCTAGCGCCACCCAG 62.682 68.421 2.29 0.00 0.00 4.45
39 40 3.712907 GAACCCTAGCGCCACCCA 61.713 66.667 2.29 0.00 0.00 4.51
40 41 4.484872 GGAACCCTAGCGCCACCC 62.485 72.222 2.29 0.00 0.00 4.61
78 79 3.077556 CTCCTCACCCCTGGGACG 61.078 72.222 16.20 4.48 38.96 4.79
79 80 2.689034 CCTCCTCACCCCTGGGAC 60.689 72.222 16.20 0.00 38.96 4.46
80 81 4.024984 CCCTCCTCACCCCTGGGA 62.025 72.222 16.20 0.00 40.23 4.37
82 83 4.024984 TCCCCTCCTCACCCCTGG 62.025 72.222 0.00 0.00 0.00 4.45
83 84 2.366167 CTCCCCTCCTCACCCCTG 60.366 72.222 0.00 0.00 0.00 4.45
84 85 2.540910 TCTCCCCTCCTCACCCCT 60.541 66.667 0.00 0.00 0.00 4.79
85 86 1.591280 TACTCTCCCCTCCTCACCCC 61.591 65.000 0.00 0.00 0.00 4.95
86 87 0.338814 TTACTCTCCCCTCCTCACCC 59.661 60.000 0.00 0.00 0.00 4.61
87 88 2.249309 TTTACTCTCCCCTCCTCACC 57.751 55.000 0.00 0.00 0.00 4.02
88 89 3.519913 ACATTTTACTCTCCCCTCCTCAC 59.480 47.826 0.00 0.00 0.00 3.51
89 90 3.803340 ACATTTTACTCTCCCCTCCTCA 58.197 45.455 0.00 0.00 0.00 3.86
90 91 4.963628 ACTACATTTTACTCTCCCCTCCTC 59.036 45.833 0.00 0.00 0.00 3.71
91 92 4.961585 ACTACATTTTACTCTCCCCTCCT 58.038 43.478 0.00 0.00 0.00 3.69
92 93 5.045797 ACAACTACATTTTACTCTCCCCTCC 60.046 44.000 0.00 0.00 0.00 4.30
93 94 6.051179 ACAACTACATTTTACTCTCCCCTC 57.949 41.667 0.00 0.00 0.00 4.30
94 95 7.563724 TTACAACTACATTTTACTCTCCCCT 57.436 36.000 0.00 0.00 0.00 4.79
95 96 8.625786 TTTTACAACTACATTTTACTCTCCCC 57.374 34.615 0.00 0.00 0.00 4.81
96 97 9.281371 ACTTTTACAACTACATTTTACTCTCCC 57.719 33.333 0.00 0.00 0.00 4.30
122 123 6.174720 ACCAAAACAGAGAGAGTTGTCATA 57.825 37.500 0.00 0.00 0.00 2.15
150 151 8.999431 CCATAAATTAGACACGGCAACTATATT 58.001 33.333 0.00 0.00 0.00 1.28
162 163 6.507456 CGCGACAACTACCATAAATTAGACAC 60.507 42.308 0.00 0.00 0.00 3.67
213 225 5.755375 CCATACATGACAACTAGGTAAGCAG 59.245 44.000 0.00 0.00 0.00 4.24
247 347 4.662278 ACTAGGTAAACACACATGGCAAT 58.338 39.130 0.00 0.00 0.00 3.56
295 395 9.440773 GCAACTATGATTCATTGGTAGATATGA 57.559 33.333 4.14 0.00 0.00 2.15
297 397 8.385491 TGGCAACTATGATTCATTGGTAGATAT 58.615 33.333 4.14 0.00 37.61 1.63
298 398 7.744733 TGGCAACTATGATTCATTGGTAGATA 58.255 34.615 4.14 0.00 37.61 1.98
308 408 4.334552 ACACACATGGCAACTATGATTCA 58.665 39.130 0.00 0.00 37.61 2.57
346 446 3.725819 AACTGCAGTTGCGCGTAA 58.274 50.000 30.66 5.23 45.83 3.18
365 465 2.718563 TGCTCGTACAGTGGTAGATGA 58.281 47.619 0.00 0.00 0.00 2.92
425 526 1.400494 GTCAACACAGTCACCAACCAC 59.600 52.381 0.00 0.00 0.00 4.16
442 543 4.668118 GCGAACCGGTTCCCGTCA 62.668 66.667 35.50 0.00 46.80 4.35
498 599 1.805945 GTTAGAGCGCTCACCCACG 60.806 63.158 36.87 0.00 0.00 4.94
536 637 2.826128 AGGAATCTGAGTGCTACGTTGA 59.174 45.455 0.00 0.00 0.00 3.18
538 639 3.963428 AAGGAATCTGAGTGCTACGTT 57.037 42.857 0.00 0.00 0.00 3.99
567 678 7.162761 TGATCCATCTTGATTTTGTTTTGCAT 58.837 30.769 0.00 0.00 0.00 3.96
577 688 5.122869 CACACGTCTTGATCCATCTTGATTT 59.877 40.000 0.00 0.00 0.00 2.17
837 952 5.019498 CGTTGTTATATGAACTTTGCGGTC 58.981 41.667 0.00 0.00 0.00 4.79
882 1032 2.202756 GAGTGGATGTCGGGCGTC 60.203 66.667 0.00 0.00 0.00 5.19
883 1033 3.771160 GGAGTGGATGTCGGGCGT 61.771 66.667 0.00 0.00 0.00 5.68
884 1034 4.873129 CGGAGTGGATGTCGGGCG 62.873 72.222 0.00 0.00 0.00 6.13
885 1035 3.458163 TCGGAGTGGATGTCGGGC 61.458 66.667 0.00 0.00 0.00 6.13
886 1036 2.494918 GTCGGAGTGGATGTCGGG 59.505 66.667 0.00 0.00 0.00 5.14
887 1037 2.494918 GGTCGGAGTGGATGTCGG 59.505 66.667 0.00 0.00 0.00 4.79
888 1038 2.102357 CGGTCGGAGTGGATGTCG 59.898 66.667 0.00 0.00 0.00 4.35
931 1082 4.595538 TTGCACGCGAGGAACCGT 62.596 61.111 15.93 0.00 38.35 4.83
938 1089 2.613739 TAGCTAGCCTTGCACGCGAG 62.614 60.000 15.93 5.97 32.80 5.03
939 1090 2.706834 TAGCTAGCCTTGCACGCGA 61.707 57.895 15.93 0.00 32.80 5.87
940 1091 2.202743 TAGCTAGCCTTGCACGCG 60.203 61.111 12.13 3.53 32.80 6.01
941 1092 0.741221 AAGTAGCTAGCCTTGCACGC 60.741 55.000 12.13 0.00 0.00 5.34
942 1093 1.002366 CAAGTAGCTAGCCTTGCACG 58.998 55.000 17.29 0.00 32.46 5.34
946 1097 0.811616 CCGGCAAGTAGCTAGCCTTG 60.812 60.000 22.35 22.35 46.14 3.61
947 1098 1.522569 CCGGCAAGTAGCTAGCCTT 59.477 57.895 17.63 5.71 46.14 4.35
1227 1419 2.359975 GGCGGGTCCAAGTCCAAG 60.360 66.667 0.00 0.00 34.01 3.61
1228 1420 3.961414 GGGCGGGTCCAAGTCCAA 61.961 66.667 2.65 0.00 36.21 3.53
1231 1423 4.754667 GTCGGGCGGGTCCAAGTC 62.755 72.222 0.00 0.00 36.21 3.01
1264 1846 3.945285 TGAAGAAACCGAACAAAGAAGCT 59.055 39.130 0.00 0.00 0.00 3.74
1415 2022 2.294233 CAGCCATGTAATTCCCAATCCG 59.706 50.000 0.00 0.00 0.00 4.18
1543 2150 3.248602 CAGAAACTCTCCCTTTTGACGTG 59.751 47.826 0.00 0.00 0.00 4.49
1707 2320 1.371758 CTCCCATACATCCGACGCG 60.372 63.158 3.53 3.53 0.00 6.01
1715 2328 6.931281 CGTTGAGACAATATTCTCCCATACAT 59.069 38.462 2.63 0.00 41.34 2.29
1724 2337 5.312120 AGTCGACGTTGAGACAATATTCT 57.688 39.130 10.46 0.00 39.67 2.40
1840 2453 1.599797 CACGAAGGGTCCGCCTTTT 60.600 57.895 0.00 0.00 33.90 2.27
1847 2460 0.179134 CTCGATGACACGAAGGGTCC 60.179 60.000 0.00 0.00 41.67 4.46
1944 2565 0.956410 CCGGTTTGGACATAACGGCA 60.956 55.000 6.32 0.00 42.00 5.69
1970 2609 7.036352 CCCATATATGAATGCCCTCCCATATAT 60.036 40.741 14.54 0.00 41.84 0.86
1971 2610 6.275381 CCCATATATGAATGCCCTCCCATATA 59.725 42.308 14.54 0.00 38.24 0.86
1972 2611 5.075483 CCCATATATGAATGCCCTCCCATAT 59.925 44.000 14.54 0.00 36.51 1.78
1973 2612 4.416513 CCCATATATGAATGCCCTCCCATA 59.583 45.833 14.54 0.00 0.00 2.74
1974 2613 3.205959 CCCATATATGAATGCCCTCCCAT 59.794 47.826 14.54 0.00 0.00 4.00
1975 2614 2.582172 CCCATATATGAATGCCCTCCCA 59.418 50.000 14.54 0.00 0.00 4.37
1976 2615 2.852449 TCCCATATATGAATGCCCTCCC 59.148 50.000 14.54 0.00 0.00 4.30
1977 2616 3.782523 TCTCCCATATATGAATGCCCTCC 59.217 47.826 14.54 0.00 0.00 4.30
1978 2617 4.141528 CCTCTCCCATATATGAATGCCCTC 60.142 50.000 14.54 0.00 0.00 4.30
1979 2618 3.784763 CCTCTCCCATATATGAATGCCCT 59.215 47.826 14.54 0.00 0.00 5.19
1980 2619 3.782523 TCCTCTCCCATATATGAATGCCC 59.217 47.826 14.54 0.00 0.00 5.36
1981 2620 5.441718 TTCCTCTCCCATATATGAATGCC 57.558 43.478 14.54 0.00 0.00 4.40
1982 2621 6.479884 AGTTTCCTCTCCCATATATGAATGC 58.520 40.000 14.54 0.00 0.00 3.56
1983 2622 7.683578 TGAGTTTCCTCTCCCATATATGAATG 58.316 38.462 14.54 2.78 38.61 2.67
1984 2623 7.878621 TGAGTTTCCTCTCCCATATATGAAT 57.121 36.000 14.54 0.00 38.61 2.57
1985 2624 7.348274 AGTTGAGTTTCCTCTCCCATATATGAA 59.652 37.037 14.54 1.28 38.61 2.57
1986 2625 6.846505 AGTTGAGTTTCCTCTCCCATATATGA 59.153 38.462 14.54 0.00 38.61 2.15
1987 2626 7.016072 AGAGTTGAGTTTCCTCTCCCATATATG 59.984 40.741 5.68 5.68 38.61 1.78
2035 2692 8.706492 TCCAATTGATTGATTTTCTGCATAAC 57.294 30.769 7.12 0.00 40.14 1.89
2082 2739 2.295885 CCCACCATCTCTGCATTTCTC 58.704 52.381 0.00 0.00 0.00 2.87
2184 4050 8.576936 AACGCTTATTCGGTTTTGAAATTAAA 57.423 26.923 0.00 0.00 0.00 1.52
2193 4059 6.183360 CCATAAGAGAACGCTTATTCGGTTTT 60.183 38.462 7.79 0.00 38.63 2.43
2203 4069 0.618458 TGGGCCATAAGAGAACGCTT 59.382 50.000 0.00 0.00 0.00 4.68
2208 4422 3.272020 AGGGAAAATGGGCCATAAGAGAA 59.728 43.478 21.54 0.00 0.00 2.87
2694 4939 4.216257 CCCAAGACATGTTTGGACTACTTG 59.784 45.833 27.44 19.93 46.42 3.16
2735 5128 7.410485 GGTAAGAGTGAGCATATTAAAACTGC 58.590 38.462 0.00 0.41 36.15 4.40
2736 5129 7.012421 GGGGTAAGAGTGAGCATATTAAAACTG 59.988 40.741 0.00 0.00 0.00 3.16
2737 5130 7.054751 GGGGTAAGAGTGAGCATATTAAAACT 58.945 38.462 0.00 0.00 0.00 2.66
2738 5131 6.262496 GGGGGTAAGAGTGAGCATATTAAAAC 59.738 42.308 0.00 0.00 0.00 2.43
2739 5132 6.362248 GGGGGTAAGAGTGAGCATATTAAAA 58.638 40.000 0.00 0.00 0.00 1.52
2740 5133 5.937111 GGGGGTAAGAGTGAGCATATTAAA 58.063 41.667 0.00 0.00 0.00 1.52
2741 5134 5.562298 GGGGGTAAGAGTGAGCATATTAA 57.438 43.478 0.00 0.00 0.00 1.40
2760 5153 1.467920 GCTCATGTGAAAAGAGGGGG 58.532 55.000 0.00 0.00 0.00 5.40
2761 5154 1.467920 GGCTCATGTGAAAAGAGGGG 58.532 55.000 0.00 0.00 0.00 4.79
2762 5155 1.089920 CGGCTCATGTGAAAAGAGGG 58.910 55.000 0.00 0.00 0.00 4.30
2763 5156 1.813513 ACGGCTCATGTGAAAAGAGG 58.186 50.000 0.00 0.00 0.00 3.69
2764 5157 2.807967 TCAACGGCTCATGTGAAAAGAG 59.192 45.455 0.00 0.00 0.00 2.85
2765 5158 2.844946 TCAACGGCTCATGTGAAAAGA 58.155 42.857 0.00 0.00 0.00 2.52
2766 5159 3.058016 ACATCAACGGCTCATGTGAAAAG 60.058 43.478 0.00 0.00 29.36 2.27
2767 5160 2.884012 ACATCAACGGCTCATGTGAAAA 59.116 40.909 0.00 0.00 29.36 2.29
2768 5161 2.483877 GACATCAACGGCTCATGTGAAA 59.516 45.455 0.00 0.00 30.71 2.69
2769 5162 2.076100 GACATCAACGGCTCATGTGAA 58.924 47.619 0.00 0.00 30.71 3.18
2770 5163 1.001860 TGACATCAACGGCTCATGTGA 59.998 47.619 0.00 0.00 30.71 3.58
2771 5164 1.441738 TGACATCAACGGCTCATGTG 58.558 50.000 0.00 0.00 30.71 3.21
2772 5165 2.408271 ATGACATCAACGGCTCATGT 57.592 45.000 0.00 0.00 33.32 3.21
2773 5166 4.880886 TTAATGACATCAACGGCTCATG 57.119 40.909 0.00 0.00 0.00 3.07
2774 5167 6.767902 ACTAATTAATGACATCAACGGCTCAT 59.232 34.615 0.00 0.00 0.00 2.90
2775 5168 6.037062 CACTAATTAATGACATCAACGGCTCA 59.963 38.462 0.00 0.00 0.00 4.26
2776 5169 6.257849 TCACTAATTAATGACATCAACGGCTC 59.742 38.462 0.00 0.00 0.00 4.70
2777 5170 6.112734 TCACTAATTAATGACATCAACGGCT 58.887 36.000 0.00 0.00 0.00 5.52
2778 5171 6.358118 TCACTAATTAATGACATCAACGGC 57.642 37.500 0.00 0.00 0.00 5.68
2803 5196 9.268282 TGAGGTAAGAAGGTAAGAGTTAATCAT 57.732 33.333 0.00 0.00 0.00 2.45
2804 5197 8.529476 GTGAGGTAAGAAGGTAAGAGTTAATCA 58.471 37.037 0.00 0.00 0.00 2.57
2805 5198 8.529476 TGTGAGGTAAGAAGGTAAGAGTTAATC 58.471 37.037 0.00 0.00 0.00 1.75
2806 5199 8.431910 TGTGAGGTAAGAAGGTAAGAGTTAAT 57.568 34.615 0.00 0.00 0.00 1.40
2807 5200 7.844493 TGTGAGGTAAGAAGGTAAGAGTTAA 57.156 36.000 0.00 0.00 0.00 2.01
2808 5201 7.453752 ACATGTGAGGTAAGAAGGTAAGAGTTA 59.546 37.037 0.00 0.00 0.00 2.24
2809 5202 6.270231 ACATGTGAGGTAAGAAGGTAAGAGTT 59.730 38.462 0.00 0.00 0.00 3.01
2810 5203 5.780793 ACATGTGAGGTAAGAAGGTAAGAGT 59.219 40.000 0.00 0.00 0.00 3.24
2811 5204 6.287589 ACATGTGAGGTAAGAAGGTAAGAG 57.712 41.667 0.00 0.00 0.00 2.85
2812 5205 7.786046 TTACATGTGAGGTAAGAAGGTAAGA 57.214 36.000 9.11 0.00 0.00 2.10
2813 5206 8.842358 TTTTACATGTGAGGTAAGAAGGTAAG 57.158 34.615 9.11 0.00 32.76 2.34
2814 5207 7.881232 CCTTTTACATGTGAGGTAAGAAGGTAA 59.119 37.037 9.11 0.00 36.13 2.85
2815 5208 7.236019 TCCTTTTACATGTGAGGTAAGAAGGTA 59.764 37.037 9.11 0.00 38.46 3.08
2816 5209 6.043938 TCCTTTTACATGTGAGGTAAGAAGGT 59.956 38.462 9.11 0.00 38.46 3.50
2817 5210 6.472887 TCCTTTTACATGTGAGGTAAGAAGG 58.527 40.000 9.11 9.20 38.54 3.46
2818 5211 6.595716 CCTCCTTTTACATGTGAGGTAAGAAG 59.404 42.308 17.20 10.35 38.22 2.85
2819 5212 6.472887 CCTCCTTTTACATGTGAGGTAAGAA 58.527 40.000 17.20 0.00 38.22 2.52
2820 5213 5.045869 CCCTCCTTTTACATGTGAGGTAAGA 60.046 44.000 21.48 5.81 40.82 2.10
2821 5214 5.186198 CCCTCCTTTTACATGTGAGGTAAG 58.814 45.833 21.48 13.62 40.82 2.34
2822 5215 4.018779 CCCCTCCTTTTACATGTGAGGTAA 60.019 45.833 21.48 1.75 40.82 2.85
2823 5216 3.521937 CCCCTCCTTTTACATGTGAGGTA 59.478 47.826 21.48 10.41 40.82 3.08
2824 5217 2.308866 CCCCTCCTTTTACATGTGAGGT 59.691 50.000 21.48 0.00 40.82 3.85
2825 5218 2.357154 CCCCCTCCTTTTACATGTGAGG 60.357 54.545 18.10 18.10 41.84 3.86
2826 5219 2.576191 TCCCCCTCCTTTTACATGTGAG 59.424 50.000 9.11 5.88 0.00 3.51
2827 5220 2.638325 TCCCCCTCCTTTTACATGTGA 58.362 47.619 9.11 0.00 0.00 3.58
2828 5221 3.449746 TTCCCCCTCCTTTTACATGTG 57.550 47.619 9.11 0.00 0.00 3.21
2829 5222 3.660669 TCTTTCCCCCTCCTTTTACATGT 59.339 43.478 2.69 2.69 0.00 3.21
2830 5223 4.273318 CTCTTTCCCCCTCCTTTTACATG 58.727 47.826 0.00 0.00 0.00 3.21
2831 5224 3.269643 CCTCTTTCCCCCTCCTTTTACAT 59.730 47.826 0.00 0.00 0.00 2.29
2832 5225 2.647802 CCTCTTTCCCCCTCCTTTTACA 59.352 50.000 0.00 0.00 0.00 2.41
2833 5226 2.025226 CCCTCTTTCCCCCTCCTTTTAC 60.025 54.545 0.00 0.00 0.00 2.01
2834 5227 2.157754 TCCCTCTTTCCCCCTCCTTTTA 60.158 50.000 0.00 0.00 0.00 1.52
2835 5228 1.084866 CCCTCTTTCCCCCTCCTTTT 58.915 55.000 0.00 0.00 0.00 2.27
2836 5229 0.198696 TCCCTCTTTCCCCCTCCTTT 59.801 55.000 0.00 0.00 0.00 3.11
2837 5230 0.253394 CTCCCTCTTTCCCCCTCCTT 60.253 60.000 0.00 0.00 0.00 3.36
2838 5231 1.398234 CTCCCTCTTTCCCCCTCCT 59.602 63.158 0.00 0.00 0.00 3.69
2839 5232 2.379459 GCTCCCTCTTTCCCCCTCC 61.379 68.421 0.00 0.00 0.00 4.30
2840 5233 0.990818 ATGCTCCCTCTTTCCCCCTC 60.991 60.000 0.00 0.00 0.00 4.30
2841 5234 1.085605 ATGCTCCCTCTTTCCCCCT 59.914 57.895 0.00 0.00 0.00 4.79
2842 5235 1.228510 CATGCTCCCTCTTTCCCCC 59.771 63.158 0.00 0.00 0.00 5.40
2843 5236 0.332972 AACATGCTCCCTCTTTCCCC 59.667 55.000 0.00 0.00 0.00 4.81
2844 5237 3.366052 TTAACATGCTCCCTCTTTCCC 57.634 47.619 0.00 0.00 0.00 3.97
2845 5238 5.921962 ATTTTAACATGCTCCCTCTTTCC 57.078 39.130 0.00 0.00 0.00 3.13
2846 5239 6.091305 GCAAATTTTAACATGCTCCCTCTTTC 59.909 38.462 0.00 0.00 35.93 2.62
2847 5240 5.934043 GCAAATTTTAACATGCTCCCTCTTT 59.066 36.000 0.00 0.00 35.93 2.52
2848 5241 5.482006 GCAAATTTTAACATGCTCCCTCTT 58.518 37.500 0.00 0.00 35.93 2.85
2849 5242 4.081476 GGCAAATTTTAACATGCTCCCTCT 60.081 41.667 0.00 0.00 38.79 3.69
2850 5243 4.183865 GGCAAATTTTAACATGCTCCCTC 58.816 43.478 0.00 0.00 38.79 4.30
2851 5244 3.582208 TGGCAAATTTTAACATGCTCCCT 59.418 39.130 0.00 0.00 38.79 4.20
2852 5245 3.936564 TGGCAAATTTTAACATGCTCCC 58.063 40.909 0.00 0.00 38.79 4.30
2853 5246 7.790823 AATATGGCAAATTTTAACATGCTCC 57.209 32.000 0.00 0.00 38.79 4.70
2876 5269 9.935241 GCTGTCAGATGGAAGAGATAATTATAA 57.065 33.333 3.32 0.00 0.00 0.98
2877 5270 8.246871 CGCTGTCAGATGGAAGAGATAATTATA 58.753 37.037 3.32 0.00 0.00 0.98
2878 5271 7.095910 CGCTGTCAGATGGAAGAGATAATTAT 58.904 38.462 3.32 0.00 0.00 1.28
2879 5272 6.450545 CGCTGTCAGATGGAAGAGATAATTA 58.549 40.000 3.32 0.00 0.00 1.40
2880 5273 5.295950 CGCTGTCAGATGGAAGAGATAATT 58.704 41.667 3.32 0.00 0.00 1.40
2881 5274 4.262377 CCGCTGTCAGATGGAAGAGATAAT 60.262 45.833 3.32 0.00 0.00 1.28
2986 5381 6.116126 GCCTATATCAAAAGAAGCCCGATAT 58.884 40.000 0.00 0.00 34.51 1.63
2990 5385 3.476552 TGCCTATATCAAAAGAAGCCCG 58.523 45.455 0.00 0.00 0.00 6.13
3044 5439 3.071457 TGGCTGATCTCTTGTGTTCAGAA 59.929 43.478 12.25 0.00 38.25 3.02
3246 5656 5.454520 GCTAAGAACTAGCGATCTAACTCC 58.545 45.833 0.00 0.00 43.64 3.85
3268 5678 7.596248 AGACAATACAAATCATGAACAAGTTGC 59.404 33.333 0.00 0.00 0.00 4.17
3288 5698 8.289939 AGAATAACTCATGATGCAAAGACAAT 57.710 30.769 0.00 0.00 0.00 2.71
3455 5867 2.364324 CAGCATATTGGATTGCAAGGCT 59.636 45.455 4.94 8.13 41.35 4.58
3480 5892 4.915809 TGGATCATCATGAAGTAGGGGAAT 59.084 41.667 0.00 0.00 0.00 3.01
3507 5919 4.712122 AATAAAACATCGGCGTCCATTT 57.288 36.364 6.85 7.66 0.00 2.32
3508 5920 4.398044 AGAAATAAAACATCGGCGTCCATT 59.602 37.500 6.85 0.00 0.00 3.16
3513 5926 3.680937 TCGAAGAAATAAAACATCGGCGT 59.319 39.130 6.85 0.00 0.00 5.68
3755 6180 6.882768 TGGCCAGGGATTTAACATAATTTT 57.117 33.333 0.00 0.00 0.00 1.82
3758 6183 5.363580 CACTTGGCCAGGGATTTAACATAAT 59.636 40.000 20.34 0.00 0.00 1.28
3760 6185 4.017958 TCACTTGGCCAGGGATTTAACATA 60.018 41.667 20.34 0.00 25.41 2.29
3761 6186 3.099141 CACTTGGCCAGGGATTTAACAT 58.901 45.455 20.34 0.00 0.00 2.71
3762 6187 2.109128 TCACTTGGCCAGGGATTTAACA 59.891 45.455 20.34 0.00 25.41 2.41
3763 6188 2.802719 TCACTTGGCCAGGGATTTAAC 58.197 47.619 20.34 0.00 25.41 2.01
3765 6190 2.378547 AGTTCACTTGGCCAGGGATTTA 59.621 45.455 20.34 0.00 33.65 1.40
3766 6191 1.147817 AGTTCACTTGGCCAGGGATTT 59.852 47.619 20.34 3.09 33.65 2.17
3897 6323 8.704234 CGTTTGCAAAGTGCCTTTTTATATTTA 58.296 29.630 13.26 0.00 44.23 1.40
3949 6375 4.716784 TCCCAGTTGTAGATGCTCTTATGT 59.283 41.667 0.00 0.00 0.00 2.29
3981 6407 1.597742 GCGTAGACGTATAGGGGTCA 58.402 55.000 11.43 0.00 42.22 4.02
3995 6421 1.658673 GGTCACTATCCGGGCGTAG 59.341 63.158 0.00 4.73 0.00 3.51
4024 6450 1.299926 AGTTCGACGTGGCAGACAC 60.300 57.895 0.00 0.00 46.78 3.67
4026 6452 2.022129 CCAGTTCGACGTGGCAGAC 61.022 63.158 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.