Multiple sequence alignment - TraesCS7A01G504200

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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 TraesCS7A01G504200 chr7A 100.000 4489 0 0 1 4489 692618267 692613779 0.000000e+00 8290.0
1 TraesCS7A01G504200 chr7A 82.635 979 143 15 2300 3260 692613244 692614213 0.000000e+00 841.0
2 TraesCS7A01G504200 chr7A 87.318 686 86 1 2574 3259 692522059 692521375 0.000000e+00 784.0
3 TraesCS7A01G504200 chr7A 87.539 321 30 4 2214 2530 692522374 692522060 3.300000e-96 363.0
4 TraesCS7A01G504200 chr7A 84.366 339 51 2 982 1318 692611285 692611623 9.310000e-87 331.0
5 TraesCS7A01G504200 chr7A 86.275 306 39 3 1037 1341 692523449 692523146 3.350000e-86 329.0
6 TraesCS7A01G504200 chr7A 91.371 197 17 0 1451 1647 692523089 692522893 2.060000e-68 270.0
7 TraesCS7A01G504200 chr7A 88.177 203 21 1 1448 1647 692762406 692762608 5.800000e-59 239.0
8 TraesCS7A01G504200 chr7A 88.824 170 19 0 2311 2480 692769979 692770148 4.550000e-50 209.0
9 TraesCS7A01G504200 chr7A 90.909 143 13 0 2009 2151 692522684 692522542 4.580000e-45 193.0
10 TraesCS7A01G504200 chr7A 78.983 295 30 19 1357 1647 692612628 692612894 5.970000e-39 172.0
11 TraesCS7A01G504200 chr7A 83.088 136 23 0 1177 1312 692762139 692762274 1.700000e-24 124.0
12 TraesCS7A01G504200 chr7A 75.646 271 37 12 176 419 692523853 692523585 1.710000e-19 108.0
13 TraesCS7A01G504200 chr7A 87.912 91 8 2 2011 2098 692800147 692800237 2.210000e-18 104.0
14 TraesCS7A01G504200 chr7B 93.588 967 61 1 2319 3284 679998626 679997660 0.000000e+00 1441.0
15 TraesCS7A01G504200 chr7B 91.120 991 48 12 1357 2323 680004812 680003838 0.000000e+00 1306.0
16 TraesCS7A01G504200 chr7B 92.008 488 39 0 4002 4489 679994305 679993818 0.000000e+00 686.0
17 TraesCS7A01G504200 chr7B 90.201 398 32 3 473 869 680005474 680005083 3.100000e-141 512.0
18 TraesCS7A01G504200 chr7B 84.752 505 68 6 2300 2802 679987815 679988312 8.670000e-137 497.0
19 TraesCS7A01G504200 chr7B 94.175 309 14 3 175 483 680005810 680005506 6.800000e-128 468.0
20 TraesCS7A01G504200 chr7B 88.963 299 33 0 1043 1341 680005094 680004796 1.970000e-98 370.0
21 TraesCS7A01G504200 chr7B 86.755 302 28 6 2236 2533 679930088 679929795 4.330000e-85 326.0
22 TraesCS7A01G504200 chr7B 90.566 212 17 3 1451 1661 680095796 680096005 1.230000e-70 278.0
23 TraesCS7A01G504200 chr7B 91.878 197 16 0 1451 1647 679987260 679987456 4.420000e-70 276.0
24 TraesCS7A01G504200 chr7B 87.826 230 28 0 1088 1317 679930999 679930770 2.060000e-68 270.0
25 TraesCS7A01G504200 chr7B 87.907 215 22 2 3782 3992 679996317 679996103 2.680000e-62 250.0
26 TraesCS7A01G504200 chr7B 82.258 248 22 1 1918 2143 679930400 679930153 1.270000e-45 195.0
27 TraesCS7A01G504200 chr7B 94.624 93 5 0 68 160 680005885 680005793 1.300000e-30 145.0
28 TraesCS7A01G504200 chr7B 85.714 126 18 0 1187 1312 680095603 680095728 2.820000e-27 134.0
29 TraesCS7A01G504200 chr7B 93.671 79 5 0 3271 3349 679997536 679997458 7.890000e-23 119.0
30 TraesCS7A01G504200 chr7D 87.446 693 72 11 3363 4048 600758024 600757340 0.000000e+00 784.0
31 TraesCS7A01G504200 chr7D 87.172 686 87 1 2574 3259 600702372 600701688 0.000000e+00 778.0
32 TraesCS7A01G504200 chr7D 95.067 446 22 0 4044 4489 600756280 600755835 0.000000e+00 702.0
33 TraesCS7A01G504200 chr7D 85.479 365 49 3 982 1344 600748357 600748719 1.180000e-100 377.0
34 TraesCS7A01G504200 chr7D 82.536 418 45 11 933 1341 600703806 600703408 4.300000e-90 342.0
35 TraesCS7A01G504200 chr7D 86.293 321 29 8 2214 2530 600702682 600702373 7.200000e-88 335.0
36 TraesCS7A01G504200 chr7D 93.909 197 12 0 1451 1647 600703332 600703136 9.440000e-77 298.0
37 TraesCS7A01G504200 chr7D 90.863 197 18 0 1451 1647 600873918 600874114 9.570000e-67 265.0
38 TraesCS7A01G504200 chr7D 91.489 188 16 0 2300 2487 600754021 600754208 4.450000e-65 259.0
39 TraesCS7A01G504200 chr7D 83.588 262 24 11 1357 1612 600748700 600748948 1.260000e-55 228.0
40 TraesCS7A01G504200 chr7D 93.007 143 10 0 2009 2151 600702930 600702788 4.550000e-50 209.0
41 TraesCS7A01G504200 chr7D 89.394 132 10 1 2008 2139 600874523 600874650 3.590000e-36 163.0
42 TraesCS7A01G504200 chr7D 84.921 126 19 0 1187 1312 600873691 600873816 1.310000e-25 128.0
43 TraesCS7A01G504200 chr3D 81.961 510 92 0 2603 3112 12299343 12298834 2.480000e-117 433.0
44 TraesCS7A01G504200 chr3D 81.961 510 92 0 2603 3112 12375492 12376001 2.480000e-117 433.0
45 TraesCS7A01G504200 chr3D 93.103 87 6 0 638 724 547439647 547439733 1.310000e-25 128.0
46 TraesCS7A01G504200 chr3D 97.436 39 0 1 472 510 13925835 13925872 1.040000e-06 65.8
47 TraesCS7A01G504200 chr3B 81.653 496 89 2 2618 3112 17782985 17782491 1.160000e-110 411.0
48 TraesCS7A01G504200 chr3B 80.784 510 98 0 2603 3112 17989525 17990034 2.520000e-107 399.0
49 TraesCS7A01G504200 chr6D 87.931 116 8 4 638 748 808290 808176 1.010000e-26 132.0
50 TraesCS7A01G504200 chr2D 91.304 92 8 0 637 728 196143352 196143443 4.710000e-25 126.0
51 TraesCS7A01G504200 chr2D 82.000 150 22 5 470 616 485745374 485745227 6.100000e-24 122.0
52 TraesCS7A01G504200 chr1B 90.526 95 9 0 638 732 572529444 572529350 4.710000e-25 126.0
53 TraesCS7A01G504200 chr3A 90.426 94 9 0 638 731 444462668 444462761 1.700000e-24 124.0
54 TraesCS7A01G504200 chr4D 91.954 87 7 0 638 724 375134933 375135019 6.100000e-24 122.0
55 TraesCS7A01G504200 chr2A 91.954 87 7 0 638 724 101846938 101847024 6.100000e-24 122.0
56 TraesCS7A01G504200 chr1A 91.954 87 7 0 637 723 539334708 539334622 6.100000e-24 122.0
57 TraesCS7A01G504200 chr6B 82.857 140 16 8 484 619 68734977 68735112 7.890000e-23 119.0
58 TraesCS7A01G504200 chr2B 81.757 148 22 5 472 618 15387876 15388019 7.890000e-23 119.0
59 TraesCS7A01G504200 chr2B 80.952 147 25 3 472 618 15392483 15392626 3.670000e-21 113.0
60 TraesCS7A01G504200 chr2B 77.632 152 25 8 472 619 448374598 448374744 2.880000e-12 84.2


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 TraesCS7A01G504200 chr7A 692613779 692618267 4488 True 8290.000000 8290 100.000000 1 4489 1 chr7A.!!$R1 4488
1 TraesCS7A01G504200 chr7A 692611285 692614213 2928 False 448.000000 841 81.994667 982 3260 3 chr7A.!!$F3 2278
2 TraesCS7A01G504200 chr7A 692521375 692523853 2478 True 341.166667 784 86.509667 176 3259 6 chr7A.!!$R2 3083
3 TraesCS7A01G504200 chr7B 679993818 679998626 4808 True 624.000000 1441 91.793500 2319 4489 4 chr7B.!!$R2 2170
4 TraesCS7A01G504200 chr7B 680003838 680005885 2047 True 560.200000 1306 91.816600 68 2323 5 chr7B.!!$R3 2255
5 TraesCS7A01G504200 chr7B 679987260 679988312 1052 False 386.500000 497 88.315000 1451 2802 2 chr7B.!!$F1 1351
6 TraesCS7A01G504200 chr7B 679929795 679930999 1204 True 263.666667 326 85.613000 1088 2533 3 chr7B.!!$R1 1445
7 TraesCS7A01G504200 chr7D 600755835 600758024 2189 True 743.000000 784 91.256500 3363 4489 2 chr7D.!!$R2 1126
8 TraesCS7A01G504200 chr7D 600701688 600703806 2118 True 392.400000 778 88.583400 933 3259 5 chr7D.!!$R1 2326
9 TraesCS7A01G504200 chr7D 600748357 600748948 591 False 302.500000 377 84.533500 982 1612 2 chr7D.!!$F2 630
10 TraesCS7A01G504200 chr3D 12298834 12299343 509 True 433.000000 433 81.961000 2603 3112 1 chr3D.!!$R1 509
11 TraesCS7A01G504200 chr3D 12375492 12376001 509 False 433.000000 433 81.961000 2603 3112 1 chr3D.!!$F1 509
12 TraesCS7A01G504200 chr3B 17989525 17990034 509 False 399.000000 399 80.784000 2603 3112 1 chr3B.!!$F1 509

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
405 431 0.108804 GACATCCGTCGCTCCTTGAA 60.109 55.0 0.00 0.0 31.07 2.69 F
1413 2526 0.179059 TTGCACGCATCCATCGGTAT 60.179 50.0 0.00 0.0 0.00 2.73 F
2793 4122 0.039180 TCGGGTGGCTCTACAAGAGA 59.961 55.0 8.11 0.0 45.07 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2913 0.240411 GCGAATAGCGACCGGAGTAT 59.760 55.0 9.46 0.0 44.57 2.12 R
2911 4240 0.320771 ATTTCGCTGGTGAGCTCGTT 60.321 50.0 9.64 0.0 43.77 3.85 R
4455 9503 0.106708 AGGCGTCTGTGCTCTTTCAA 59.893 50.0 0.00 0.0 34.52 2.69 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
26 27 8.873215 ACGACACCTACAAATTTAGATCATAG 57.127 34.615 0.00 0.00 0.00 2.23
27 28 8.692710 ACGACACCTACAAATTTAGATCATAGA 58.307 33.333 0.00 0.00 0.00 1.98
28 29 8.969267 CGACACCTACAAATTTAGATCATAGAC 58.031 37.037 0.00 0.00 0.00 2.59
29 30 8.873215 ACACCTACAAATTTAGATCATAGACG 57.127 34.615 0.00 0.00 0.00 4.18
30 31 8.475639 ACACCTACAAATTTAGATCATAGACGT 58.524 33.333 0.00 0.00 0.00 4.34
31 32 8.755941 CACCTACAAATTTAGATCATAGACGTG 58.244 37.037 0.00 0.00 0.00 4.49
32 33 8.692710 ACCTACAAATTTAGATCATAGACGTGA 58.307 33.333 0.00 0.00 0.00 4.35
33 34 8.969267 CCTACAAATTTAGATCATAGACGTGAC 58.031 37.037 0.00 0.00 0.00 3.67
34 35 7.772332 ACAAATTTAGATCATAGACGTGACC 57.228 36.000 0.00 0.00 0.00 4.02
35 36 7.556844 ACAAATTTAGATCATAGACGTGACCT 58.443 34.615 0.00 0.00 0.00 3.85
36 37 7.707035 ACAAATTTAGATCATAGACGTGACCTC 59.293 37.037 0.00 0.00 0.00 3.85
37 38 6.961360 ATTTAGATCATAGACGTGACCTCA 57.039 37.500 0.00 0.00 0.00 3.86
38 39 5.752892 TTAGATCATAGACGTGACCTCAC 57.247 43.478 0.00 0.00 43.15 3.51
39 40 3.892284 AGATCATAGACGTGACCTCACT 58.108 45.455 0.00 0.00 44.34 3.41
40 41 3.629855 AGATCATAGACGTGACCTCACTG 59.370 47.826 0.00 0.84 44.34 3.66
41 42 3.067684 TCATAGACGTGACCTCACTGA 57.932 47.619 0.00 0.00 44.34 3.41
42 43 3.418047 TCATAGACGTGACCTCACTGAA 58.582 45.455 0.00 0.00 44.34 3.02
43 44 4.017126 TCATAGACGTGACCTCACTGAAT 58.983 43.478 0.00 0.00 44.34 2.57
44 45 4.462834 TCATAGACGTGACCTCACTGAATT 59.537 41.667 0.00 0.00 44.34 2.17
45 46 3.753294 AGACGTGACCTCACTGAATTT 57.247 42.857 0.00 0.00 44.34 1.82
46 47 4.073293 AGACGTGACCTCACTGAATTTT 57.927 40.909 0.00 0.00 44.34 1.82
47 48 3.809832 AGACGTGACCTCACTGAATTTTG 59.190 43.478 0.00 0.00 44.34 2.44
48 49 2.290641 ACGTGACCTCACTGAATTTTGC 59.709 45.455 4.00 0.00 44.34 3.68
49 50 2.549754 CGTGACCTCACTGAATTTTGCT 59.450 45.455 4.00 0.00 44.34 3.91
50 51 3.003689 CGTGACCTCACTGAATTTTGCTT 59.996 43.478 4.00 0.00 44.34 3.91
51 52 4.498009 CGTGACCTCACTGAATTTTGCTTT 60.498 41.667 4.00 0.00 44.34 3.51
52 53 4.978580 GTGACCTCACTGAATTTTGCTTTC 59.021 41.667 0.00 0.00 43.25 2.62
53 54 4.644234 TGACCTCACTGAATTTTGCTTTCA 59.356 37.500 0.00 0.00 0.00 2.69
54 55 5.126869 TGACCTCACTGAATTTTGCTTTCAA 59.873 36.000 0.00 0.00 32.98 2.69
55 56 5.976458 ACCTCACTGAATTTTGCTTTCAAA 58.024 33.333 0.00 0.00 40.17 2.69
70 71 5.994668 TGCTTTCAAAAAGAACCAAAACTGT 59.005 32.000 3.68 0.00 35.56 3.55
82 83 3.573967 ACCAAAACTGTGCAAATAGGAGG 59.426 43.478 0.00 0.00 0.00 4.30
85 86 0.392998 ACTGTGCAAATAGGAGGGCG 60.393 55.000 0.00 0.00 0.00 6.13
88 89 3.953887 GCAAATAGGAGGGCGCGC 61.954 66.667 25.94 25.94 0.00 6.86
131 132 1.117150 GGCTATGGGTTCGAGTACCA 58.883 55.000 8.50 7.81 40.09 3.25
142 143 4.392138 GGTTCGAGTACCAATGAGGAAAAG 59.608 45.833 1.23 0.00 41.22 2.27
143 144 5.235516 GTTCGAGTACCAATGAGGAAAAGA 58.764 41.667 0.00 0.00 41.22 2.52
144 145 5.677319 TCGAGTACCAATGAGGAAAAGAT 57.323 39.130 0.00 0.00 41.22 2.40
145 146 6.785337 TCGAGTACCAATGAGGAAAAGATA 57.215 37.500 0.00 0.00 41.22 1.98
146 147 7.177832 TCGAGTACCAATGAGGAAAAGATAA 57.822 36.000 0.00 0.00 41.22 1.75
147 148 7.039882 TCGAGTACCAATGAGGAAAAGATAAC 58.960 38.462 0.00 0.00 41.22 1.89
148 149 6.019801 CGAGTACCAATGAGGAAAAGATAACG 60.020 42.308 0.00 0.00 41.22 3.18
149 150 6.708285 AGTACCAATGAGGAAAAGATAACGT 58.292 36.000 0.00 0.00 41.22 3.99
150 151 5.880054 ACCAATGAGGAAAAGATAACGTG 57.120 39.130 0.00 0.00 41.22 4.49
151 152 5.313712 ACCAATGAGGAAAAGATAACGTGT 58.686 37.500 0.00 0.00 41.22 4.49
152 153 5.411669 ACCAATGAGGAAAAGATAACGTGTC 59.588 40.000 0.00 0.00 41.22 3.67
153 154 5.445939 CCAATGAGGAAAAGATAACGTGTCG 60.446 44.000 0.00 0.00 41.22 4.35
154 155 2.991190 TGAGGAAAAGATAACGTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
155 156 3.251571 GAGGAAAAGATAACGTGTCGCT 58.748 45.455 0.00 0.00 0.00 4.93
156 157 3.660865 AGGAAAAGATAACGTGTCGCTT 58.339 40.909 0.00 0.00 0.00 4.68
157 158 3.678548 AGGAAAAGATAACGTGTCGCTTC 59.321 43.478 0.00 0.00 0.00 3.86
158 159 3.678548 GGAAAAGATAACGTGTCGCTTCT 59.321 43.478 0.00 0.00 0.00 2.85
159 160 4.151867 GGAAAAGATAACGTGTCGCTTCTT 59.848 41.667 0.00 0.00 0.00 2.52
160 161 5.333875 GGAAAAGATAACGTGTCGCTTCTTT 60.334 40.000 0.00 0.00 35.66 2.52
161 162 5.668558 AAAGATAACGTGTCGCTTCTTTT 57.331 34.783 0.00 0.00 32.77 2.27
162 163 5.668558 AAGATAACGTGTCGCTTCTTTTT 57.331 34.783 0.00 0.00 0.00 1.94
392 418 2.045926 AAGCGGTGCCTGACATCC 60.046 61.111 0.00 0.00 0.00 3.51
405 431 0.108804 GACATCCGTCGCTCCTTGAA 60.109 55.000 0.00 0.00 31.07 2.69
433 459 6.435292 ACTTCTTCATACCCACTTGTACTT 57.565 37.500 0.00 0.00 0.00 2.24
434 460 6.838382 ACTTCTTCATACCCACTTGTACTTT 58.162 36.000 0.00 0.00 0.00 2.66
435 461 6.935208 ACTTCTTCATACCCACTTGTACTTTC 59.065 38.462 0.00 0.00 0.00 2.62
440 466 7.739498 TCATACCCACTTGTACTTTCTTTTC 57.261 36.000 0.00 0.00 0.00 2.29
465 491 5.044558 GCATAAGAAGAGACTACCTTTCCG 58.955 45.833 0.00 0.00 0.00 4.30
547 614 5.063438 ACATACATTCGTCCAACATTCTTCG 59.937 40.000 0.00 0.00 0.00 3.79
560 627 9.389755 TCCAACATTCTTCGTATGATAATCAAA 57.610 29.630 0.00 0.00 0.00 2.69
738 806 6.038997 AGGGAGTATAAGATAAATCACCGC 57.961 41.667 0.00 0.00 0.00 5.68
751 819 9.295825 AGATAAATCACCGCCATAATTTGATAA 57.704 29.630 0.00 0.00 0.00 1.75
756 824 7.106439 TCACCGCCATAATTTGATAAACATT 57.894 32.000 0.00 0.00 0.00 2.71
803 871 7.878477 TGAGTAGGTAAATCACAAACTAACG 57.122 36.000 0.00 0.00 0.00 3.18
808 876 9.962759 GTAGGTAAATCACAAACTAACGTATTG 57.037 33.333 0.00 0.00 0.00 1.90
827 895 9.204570 ACGTATTGGACTATTTATATCTGTTGC 57.795 33.333 0.00 0.00 0.00 4.17
834 902 8.517878 GGACTATTTATATCTGTTGCAATGCAT 58.482 33.333 9.39 0.00 38.76 3.96
835 903 9.338291 GACTATTTATATCTGTTGCAATGCATG 57.662 33.333 9.39 2.82 38.76 4.06
836 904 8.301720 ACTATTTATATCTGTTGCAATGCATGG 58.698 33.333 9.39 0.00 38.76 3.66
837 905 5.456548 TTATATCTGTTGCAATGCATGGG 57.543 39.130 9.39 2.07 38.76 4.00
838 906 1.563924 ATCTGTTGCAATGCATGGGT 58.436 45.000 9.39 0.00 38.76 4.51
847 915 4.989277 TGCAATGCATGGGTATTATCTCT 58.011 39.130 2.72 0.00 31.71 3.10
857 925 9.944376 GCATGGGTATTATCTCTGTCTATTAAA 57.056 33.333 0.00 0.00 0.00 1.52
869 937 9.284968 TCTCTGTCTATTAAAGAAACCTTTTGG 57.715 33.333 0.00 0.00 40.11 3.28
886 954 7.576861 CCTTTTGGTTAGACCTAAGAACAAA 57.423 36.000 11.52 8.71 39.58 2.83
887 955 7.423199 CCTTTTGGTTAGACCTAAGAACAAAC 58.577 38.462 11.52 0.00 39.58 2.93
888 956 7.284716 CCTTTTGGTTAGACCTAAGAACAAACT 59.715 37.037 11.52 0.00 39.58 2.66
889 957 9.333724 CTTTTGGTTAGACCTAAGAACAAACTA 57.666 33.333 10.83 0.00 39.58 2.24
890 958 8.667076 TTTGGTTAGACCTAAGAACAAACTAC 57.333 34.615 0.00 0.00 39.58 2.73
891 959 7.364149 TGGTTAGACCTAAGAACAAACTACA 57.636 36.000 0.00 0.00 39.58 2.74
892 960 7.794041 TGGTTAGACCTAAGAACAAACTACAA 58.206 34.615 0.00 0.00 39.58 2.41
893 961 7.712205 TGGTTAGACCTAAGAACAAACTACAAC 59.288 37.037 0.00 0.00 39.58 3.32
894 962 7.712205 GGTTAGACCTAAGAACAAACTACAACA 59.288 37.037 0.00 0.00 34.73 3.33
895 963 9.269453 GTTAGACCTAAGAACAAACTACAACAT 57.731 33.333 0.00 0.00 0.00 2.71
898 966 9.841295 AGACCTAAGAACAAACTACAACATAAA 57.159 29.630 0.00 0.00 0.00 1.40
918 986 8.803235 ACATAAAATAAAAGGAGAAAGTGACCC 58.197 33.333 0.00 0.00 0.00 4.46
919 987 8.802267 CATAAAATAAAAGGAGAAAGTGACCCA 58.198 33.333 0.00 0.00 0.00 4.51
920 988 6.650427 AAATAAAAGGAGAAAGTGACCCAC 57.350 37.500 0.00 0.00 34.10 4.61
996 1064 3.601685 TCCGCGAGCGCATCCATA 61.602 61.111 11.47 0.00 42.06 2.74
998 1066 3.756677 CGCGAGCGCATCCATACG 61.757 66.667 11.47 4.62 42.06 3.06
1023 1092 5.008019 ACCATTTAAAGCTACTGCATCATCG 59.992 40.000 0.00 0.00 42.74 3.84
1075 1178 1.208165 AAGCCAAGGGATCTCGGGTT 61.208 55.000 7.98 3.51 34.50 4.11
1079 1182 2.619590 GCCAAGGGATCTCGGGTTTTAA 60.620 50.000 7.98 0.00 0.00 1.52
1086 1189 4.157289 GGGATCTCGGGTTTTAAAAGTTCC 59.843 45.833 0.00 3.54 0.00 3.62
1107 1210 1.144936 GCTAGAGCGGAACCATGCT 59.855 57.895 0.00 0.00 45.90 3.79
1291 1394 0.679640 CCGGCACCATCCTTGCTTTA 60.680 55.000 0.00 0.00 40.07 1.85
1328 2429 8.476447 AGCTCCAGGTTACTAATAACTAAGTTC 58.524 37.037 0.00 0.00 40.59 3.01
1332 2433 8.755977 CCAGGTTACTAATAACTAAGTTCTCCA 58.244 37.037 0.00 0.00 40.59 3.86
1410 2523 2.108514 ACTTGCACGCATCCATCGG 61.109 57.895 0.00 0.00 0.00 4.18
1412 2525 0.809636 CTTGCACGCATCCATCGGTA 60.810 55.000 0.00 0.00 0.00 4.02
1413 2526 0.179059 TTGCACGCATCCATCGGTAT 60.179 50.000 0.00 0.00 0.00 2.73
1414 2527 0.676736 TGCACGCATCCATCGGTATA 59.323 50.000 0.00 0.00 0.00 1.47
1428 2541 9.601810 ATCCATCGGTATATATATATGGTGTGT 57.398 33.333 20.31 10.38 0.00 3.72
1441 2554 1.742831 TGGTGTGTTTGAGCAGTTGTC 59.257 47.619 0.00 0.00 0.00 3.18
1443 2556 1.396996 GTGTGTTTGAGCAGTTGTCGT 59.603 47.619 0.00 0.00 0.00 4.34
1446 2559 0.317020 GTTTGAGCAGTTGTCGTGGC 60.317 55.000 0.00 0.00 0.00 5.01
1463 2576 2.580867 CTGCGTGCGTAGGAGCTC 60.581 66.667 4.71 4.71 38.13 4.09
1683 2796 3.659444 GCATACTTTTAAATAGCGCGCTG 59.341 43.478 41.85 24.99 0.00 5.18
1794 2907 9.618890 ATTTGTCATGCTATAGTGTCAACTTAT 57.381 29.630 0.84 0.00 37.88 1.73
1800 2913 2.640346 TAGTGTCAACTTATCGCGCA 57.360 45.000 8.75 0.00 37.88 6.09
1801 2914 2.010145 AGTGTCAACTTATCGCGCAT 57.990 45.000 8.75 2.59 30.14 4.73
1803 2916 2.858344 AGTGTCAACTTATCGCGCATAC 59.142 45.455 8.75 0.00 30.14 2.39
1804 2917 2.858344 GTGTCAACTTATCGCGCATACT 59.142 45.455 8.75 0.00 0.00 2.12
1831 2946 4.986659 GTCGCTATTCGCCCTTCTATTTAA 59.013 41.667 0.00 0.00 38.27 1.52
1868 2983 5.651530 ACTCTGTGAACACATATAAGACGG 58.348 41.667 8.09 0.00 41.01 4.79
1901 3016 8.598202 TTGTTTACACAGGGAGTATATGACTA 57.402 34.615 0.00 0.00 34.22 2.59
1904 3019 5.068215 ACACAGGGAGTATATGACTAGCT 57.932 43.478 0.00 0.00 39.06 3.32
1958 3132 8.798859 ACTCATGAGCTATTTACAATCTGTTT 57.201 30.769 22.83 0.00 0.00 2.83
1978 3152 1.380380 GCAGCAAAGGGCCTATGGT 60.380 57.895 6.41 1.90 46.50 3.55
2068 3264 4.763793 CAGACCCTCAAGAACATTGTCATT 59.236 41.667 0.00 0.00 0.00 2.57
2107 3303 2.122768 CTCCTCCAGCCTACCATCTTT 58.877 52.381 0.00 0.00 0.00 2.52
2172 3385 5.751509 CCATAGTGGCATGTCATTCAAATTG 59.248 40.000 1.89 0.00 0.00 2.32
2246 3558 1.737735 CAAGCGATGCAGTGACCGA 60.738 57.895 0.00 0.00 0.00 4.69
2323 3636 3.689161 CGAAATTTGTACAGGCCATGAGA 59.311 43.478 5.01 0.00 0.00 3.27
2375 3688 2.817834 GCATTAGCACGTCCGCCA 60.818 61.111 0.00 0.00 41.58 5.69
2593 3922 4.262079 GCGCCTCACTAACTTATATGGACT 60.262 45.833 0.00 0.00 0.00 3.85
2626 3955 1.302431 CTGTTGGCGATGACCCACA 60.302 57.895 0.00 0.00 30.65 4.17
2669 3998 1.529744 AACCTGGACTTCTTCCCCAA 58.470 50.000 0.00 0.00 45.17 4.12
2732 4061 2.104331 CGGCACCGCTAAGATCGT 59.896 61.111 0.00 0.00 0.00 3.73
2749 4078 3.358707 TCGTAGAGAAGTTTGACGCAA 57.641 42.857 0.00 0.00 33.64 4.85
2750 4079 3.909430 TCGTAGAGAAGTTTGACGCAAT 58.091 40.909 0.00 0.00 33.64 3.56
2793 4122 0.039180 TCGGGTGGCTCTACAAGAGA 59.961 55.000 8.11 0.00 45.07 3.10
2834 4163 1.216710 GCTTCAGCGAGGCTAGTGT 59.783 57.895 5.63 0.00 36.40 3.55
2890 4219 1.076777 ACCCTGCACTGCAACAAGT 60.077 52.632 4.99 0.00 38.41 3.16
2911 4240 2.158519 TGCTATCTCCGGATCCAGTACA 60.159 50.000 13.41 0.00 33.71 2.90
2923 4252 0.317160 CCAGTACAACGAGCTCACCA 59.683 55.000 15.40 0.00 0.00 4.17
3001 4330 1.153958 GGCAAAGCGCTGCTAAAGG 60.154 57.895 12.58 0.00 42.25 3.11
3035 4364 0.388649 ATGAACGTCGAGACAGGCAC 60.389 55.000 0.00 0.00 0.00 5.01
3061 4390 1.367840 CCCGATCTAAAGAGGGGCG 59.632 63.158 6.09 0.00 40.18 6.13
3093 4422 2.433436 GAACTAGTCCATTTTGCCCGT 58.567 47.619 0.00 0.00 0.00 5.28
3114 4443 2.430244 TTGTCGGAAGAGCGCGAC 60.430 61.111 12.10 2.22 43.49 5.19
3137 4472 0.250553 CGGAAGGTGGGCTACAAACA 60.251 55.000 2.66 0.00 0.00 2.83
3195 4537 3.554934 TGACCCTTGCATGTTGGATATC 58.445 45.455 0.00 0.00 0.00 1.63
3310 4790 9.063615 ACTCAAGAAAATAATACTCGTGGTTTT 57.936 29.630 0.00 0.00 0.00 2.43
3349 4829 0.613260 AGAGCAGTACATGGCGGAAA 59.387 50.000 0.00 0.00 34.54 3.13
3350 4830 0.727398 GAGCAGTACATGGCGGAAAC 59.273 55.000 0.00 0.00 34.54 2.78
3351 4831 0.036164 AGCAGTACATGGCGGAAACA 59.964 50.000 0.00 0.00 34.54 2.83
3352 4832 0.878416 GCAGTACATGGCGGAAACAA 59.122 50.000 0.00 0.00 0.00 2.83
3353 4833 1.268352 GCAGTACATGGCGGAAACAAA 59.732 47.619 0.00 0.00 0.00 2.83
3354 4834 2.920647 GCAGTACATGGCGGAAACAAAC 60.921 50.000 0.00 0.00 0.00 2.93
3355 4835 1.533731 AGTACATGGCGGAAACAAACG 59.466 47.619 0.00 0.00 0.00 3.60
3373 4889 3.923017 ACGCTCCTGAAATTCTTTTGG 57.077 42.857 0.00 0.00 0.00 3.28
3399 4915 3.478857 TTAGGAACAAACGCTCCTGAA 57.521 42.857 0.79 0.00 42.25 3.02
3406 4923 5.276820 GGAACAAACGCTCCTGAAATTTTTG 60.277 40.000 0.00 0.00 0.00 2.44
3411 4928 7.065683 ACAAACGCTCCTGAAATTTTTGAAATT 59.934 29.630 0.00 0.00 0.00 1.82
3422 4939 9.346725 TGAAATTTTTGAAATTTTTGGAAACCG 57.653 25.926 11.39 0.00 30.68 4.44
3424 4941 7.631717 ATTTTTGAAATTTTTGGAAACCGGA 57.368 28.000 9.46 0.00 0.00 5.14
3494 5011 1.052124 TAGGTTGATTCGGCCCGGAT 61.052 55.000 0.73 0.00 0.00 4.18
3505 5022 0.668535 GGCCCGGATTTTAGTCATGC 59.331 55.000 0.73 0.00 0.00 4.06
3519 5259 2.954318 AGTCATGCTTTTGTGTGAGCTT 59.046 40.909 0.00 0.00 39.60 3.74
3525 5265 1.331756 CTTTTGTGTGAGCTTGCGACT 59.668 47.619 0.00 0.00 0.00 4.18
3538 5278 4.339530 AGCTTGCGACTATGATAAGACTCA 59.660 41.667 0.00 0.00 0.00 3.41
3541 5281 4.550422 TGCGACTATGATAAGACTCATGC 58.450 43.478 0.00 0.00 36.55 4.06
3552 5292 3.547567 ACTCATGCCAGAGTTGAGC 57.452 52.632 2.57 0.00 46.26 4.26
3553 5293 0.982704 ACTCATGCCAGAGTTGAGCT 59.017 50.000 2.57 0.00 46.26 4.09
3575 5315 6.330250 AGCTTGTGATACCAATACCCTCTATT 59.670 38.462 0.00 0.00 0.00 1.73
3582 5651 4.781934 ACCAATACCCTCTATTCAACTGC 58.218 43.478 0.00 0.00 0.00 4.40
3593 5662 5.136828 TCTATTCAACTGCCTTTTTGGTGA 58.863 37.500 0.00 0.00 38.35 4.02
3597 5666 1.708341 ACTGCCTTTTTGGTGATGCT 58.292 45.000 0.00 0.00 38.35 3.79
3599 5668 2.558359 ACTGCCTTTTTGGTGATGCTAC 59.442 45.455 0.00 0.00 38.35 3.58
3601 5670 3.230134 TGCCTTTTTGGTGATGCTACTT 58.770 40.909 0.00 0.00 38.35 2.24
3611 5680 6.493189 TGGTGATGCTACTTACAATATCCA 57.507 37.500 0.00 0.00 0.00 3.41
3658 5727 8.898761 ACTCACAATGTTGAGACTAGACTATAG 58.101 37.037 15.92 0.00 45.19 1.31
3671 5740 9.787435 AGACTAGACTATAGAGACCTATTTGTG 57.213 37.037 6.78 0.00 36.93 3.33
3684 5753 4.700213 ACCTATTTGTGGACTCAATTTCCG 59.300 41.667 0.00 0.00 35.70 4.30
3700 5769 8.514136 TCAATTTCCGTGTGTTTGATTATTTC 57.486 30.769 0.00 0.00 0.00 2.17
3710 5780 6.915300 TGTGTTTGATTATTTCACTGTTTCCG 59.085 34.615 0.00 0.00 32.84 4.30
3711 5781 7.136119 GTGTTTGATTATTTCACTGTTTCCGA 58.864 34.615 0.00 0.00 32.84 4.55
3735 5805 5.337578 AAAACATGTAACACCAAGCAACT 57.662 34.783 0.00 0.00 0.00 3.16
3739 5809 5.827666 ACATGTAACACCAAGCAACTTAAC 58.172 37.500 0.00 0.00 0.00 2.01
3764 5834 8.646900 ACTAACCATGATAAAATGTGTTGGTTT 58.353 29.630 9.44 0.00 41.83 3.27
3766 5836 7.727331 ACCATGATAAAATGTGTTGGTTTTG 57.273 32.000 0.00 0.00 32.23 2.44
3774 5844 9.912634 ATAAAATGTGTTGGTTTTGAGTCTATG 57.087 29.630 0.00 0.00 0.00 2.23
3794 5986 7.697291 GTCTATGTACTAGTTTCTAGCACACAC 59.303 40.741 0.00 6.19 0.00 3.82
3851 6043 0.534203 CACGTGGGTTAACAGCCTGT 60.534 55.000 7.95 0.00 41.69 4.00
3879 6071 5.502869 GCTGATCTTGCAAAACAAAACCAAG 60.503 40.000 0.00 0.00 37.96 3.61
3885 6077 5.604010 TGCAAAACAAAACCAAGTCTTTG 57.396 34.783 0.00 0.00 38.29 2.77
3899 6093 3.654273 AGTCTTTGGCCCTATACTGCTA 58.346 45.455 0.00 0.00 0.00 3.49
3952 6146 7.878477 ACTCAATTTGCATGTGTTTATTCTG 57.122 32.000 0.00 0.00 0.00 3.02
3976 6170 6.714810 TGTATTGTATTCCAGCATAACCATCC 59.285 38.462 0.00 0.00 0.00 3.51
3998 6192 5.044624 TCCTAGGCACCTTGAGTACTACTTA 60.045 44.000 2.96 0.00 0.00 2.24
3999 6193 5.067544 CCTAGGCACCTTGAGTACTACTTAC 59.932 48.000 0.00 0.00 0.00 2.34
4141 9189 7.750229 AAATATCCAACAGGCATACATACAG 57.250 36.000 0.00 0.00 0.00 2.74
4157 9205 9.356433 CATACATACAGCATCAAATTCAAACAA 57.644 29.630 0.00 0.00 0.00 2.83
4227 9275 2.109126 GGCTTTGCGCTCTTCCGAT 61.109 57.895 9.73 0.00 39.13 4.18
4236 9284 0.598680 GCTCTTCCGATAGCATGCGT 60.599 55.000 13.01 5.03 38.63 5.24
4259 9307 1.716028 AAACGGGCCAGTTCCTCCTT 61.716 55.000 21.96 1.90 32.43 3.36
4322 9370 0.394938 ACGTTCACCATGCACACCTA 59.605 50.000 0.00 0.00 0.00 3.08
4336 9384 2.028112 CACACCTACCTCTTTAGCAGCA 60.028 50.000 0.00 0.00 0.00 4.41
4344 9392 1.375908 CTTTAGCAGCACCTCGCCA 60.376 57.895 0.00 0.00 44.04 5.69
4348 9396 2.786539 TAGCAGCACCTCGCCAACAG 62.787 60.000 0.00 0.00 44.04 3.16
4367 9415 1.926511 GCAATGAGCCCGTTGAGGTG 61.927 60.000 4.08 0.00 40.79 4.00
4455 9503 0.947244 GCTTGTTGCAGTGTAGTGCT 59.053 50.000 12.43 0.00 44.32 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.961265 CTATGATCTAAATTTGTAGGTGTCGTA 57.039 33.333 0.00 0.00 0.00 3.43
1 2 8.692710 TCTATGATCTAAATTTGTAGGTGTCGT 58.307 33.333 0.00 0.00 0.00 4.34
2 3 8.969267 GTCTATGATCTAAATTTGTAGGTGTCG 58.031 37.037 0.00 0.00 0.00 4.35
3 4 8.969267 CGTCTATGATCTAAATTTGTAGGTGTC 58.031 37.037 0.00 0.00 0.00 3.67
4 5 8.475639 ACGTCTATGATCTAAATTTGTAGGTGT 58.524 33.333 0.00 0.00 0.00 4.16
5 6 8.755941 CACGTCTATGATCTAAATTTGTAGGTG 58.244 37.037 0.00 0.00 0.00 4.00
6 7 8.692710 TCACGTCTATGATCTAAATTTGTAGGT 58.307 33.333 0.00 0.00 0.00 3.08
7 8 8.969267 GTCACGTCTATGATCTAAATTTGTAGG 58.031 37.037 0.00 0.00 0.00 3.18
8 9 8.969267 GGTCACGTCTATGATCTAAATTTGTAG 58.031 37.037 0.00 0.00 0.00 2.74
9 10 8.692710 AGGTCACGTCTATGATCTAAATTTGTA 58.307 33.333 0.00 0.00 38.33 2.41
10 11 7.556844 AGGTCACGTCTATGATCTAAATTTGT 58.443 34.615 0.00 0.00 38.33 2.83
11 12 7.706607 TGAGGTCACGTCTATGATCTAAATTTG 59.293 37.037 0.00 0.00 40.26 2.32
12 13 7.707035 GTGAGGTCACGTCTATGATCTAAATTT 59.293 37.037 0.00 0.00 40.26 1.82
13 14 7.203910 GTGAGGTCACGTCTATGATCTAAATT 58.796 38.462 0.00 0.00 40.26 1.82
14 15 6.740110 GTGAGGTCACGTCTATGATCTAAAT 58.260 40.000 0.00 0.00 40.26 1.40
15 16 6.132791 GTGAGGTCACGTCTATGATCTAAA 57.867 41.667 0.00 0.00 40.26 1.85
16 17 5.752892 GTGAGGTCACGTCTATGATCTAA 57.247 43.478 0.00 0.00 40.26 2.10
29 30 4.574599 AAGCAAAATTCAGTGAGGTCAC 57.425 40.909 1.60 1.60 46.77 3.67
30 31 4.644234 TGAAAGCAAAATTCAGTGAGGTCA 59.356 37.500 0.00 0.00 33.15 4.02
31 32 5.186996 TGAAAGCAAAATTCAGTGAGGTC 57.813 39.130 0.00 0.00 33.15 3.85
32 33 5.596836 TTGAAAGCAAAATTCAGTGAGGT 57.403 34.783 0.00 0.00 38.01 3.85
33 34 6.907206 TTTTGAAAGCAAAATTCAGTGAGG 57.093 33.333 0.00 0.00 46.09 3.86
44 45 7.012799 ACAGTTTTGGTTCTTTTTGAAAGCAAA 59.987 29.630 8.00 8.00 41.97 3.68
45 46 6.484977 ACAGTTTTGGTTCTTTTTGAAAGCAA 59.515 30.769 0.00 0.00 36.30 3.91
46 47 5.994668 ACAGTTTTGGTTCTTTTTGAAAGCA 59.005 32.000 0.00 0.00 36.30 3.91
47 48 6.306397 CACAGTTTTGGTTCTTTTTGAAAGC 58.694 36.000 0.00 0.00 36.30 3.51
48 49 6.073331 TGCACAGTTTTGGTTCTTTTTGAAAG 60.073 34.615 0.00 0.00 36.30 2.62
49 50 5.760253 TGCACAGTTTTGGTTCTTTTTGAAA 59.240 32.000 0.00 0.00 36.30 2.69
50 51 5.300752 TGCACAGTTTTGGTTCTTTTTGAA 58.699 33.333 0.00 0.00 0.00 2.69
51 52 4.887748 TGCACAGTTTTGGTTCTTTTTGA 58.112 34.783 0.00 0.00 0.00 2.69
52 53 5.604010 TTGCACAGTTTTGGTTCTTTTTG 57.396 34.783 0.00 0.00 0.00 2.44
53 54 6.816134 ATTTGCACAGTTTTGGTTCTTTTT 57.184 29.167 0.00 0.00 0.00 1.94
54 55 6.538381 CCTATTTGCACAGTTTTGGTTCTTTT 59.462 34.615 0.00 0.00 0.00 2.27
55 56 6.048509 CCTATTTGCACAGTTTTGGTTCTTT 58.951 36.000 0.00 0.00 0.00 2.52
56 57 5.362430 TCCTATTTGCACAGTTTTGGTTCTT 59.638 36.000 0.00 0.00 0.00 2.52
57 58 4.892934 TCCTATTTGCACAGTTTTGGTTCT 59.107 37.500 0.00 0.00 0.00 3.01
58 59 5.195001 TCCTATTTGCACAGTTTTGGTTC 57.805 39.130 0.00 0.00 0.00 3.62
59 60 4.039124 CCTCCTATTTGCACAGTTTTGGTT 59.961 41.667 0.00 0.00 0.00 3.67
60 61 3.573967 CCTCCTATTTGCACAGTTTTGGT 59.426 43.478 0.00 0.00 0.00 3.67
61 62 3.056607 CCCTCCTATTTGCACAGTTTTGG 60.057 47.826 0.00 0.00 0.00 3.28
62 63 3.614870 GCCCTCCTATTTGCACAGTTTTG 60.615 47.826 0.00 0.00 0.00 2.44
63 64 2.562738 GCCCTCCTATTTGCACAGTTTT 59.437 45.455 0.00 0.00 0.00 2.43
64 65 2.171003 GCCCTCCTATTTGCACAGTTT 58.829 47.619 0.00 0.00 0.00 2.66
65 66 1.839424 GCCCTCCTATTTGCACAGTT 58.161 50.000 0.00 0.00 0.00 3.16
66 67 0.392998 CGCCCTCCTATTTGCACAGT 60.393 55.000 0.00 0.00 0.00 3.55
70 71 2.513666 CGCGCCCTCCTATTTGCA 60.514 61.111 0.00 0.00 0.00 4.08
82 83 1.687494 GAATATCGGATGAGCGCGCC 61.687 60.000 30.33 19.97 0.00 6.53
85 86 1.461127 GTTGGAATATCGGATGAGCGC 59.539 52.381 0.00 0.00 0.00 5.92
88 89 2.069273 GCGGTTGGAATATCGGATGAG 58.931 52.381 0.00 0.00 0.00 2.90
131 132 4.092968 GCGACACGTTATCTTTTCCTCATT 59.907 41.667 0.00 0.00 0.00 2.57
164 165 4.212425 AGCGACACGTTATCACATCAAAAA 59.788 37.500 0.00 0.00 0.00 1.94
165 166 3.743911 AGCGACACGTTATCACATCAAAA 59.256 39.130 0.00 0.00 0.00 2.44
166 167 3.322369 AGCGACACGTTATCACATCAAA 58.678 40.909 0.00 0.00 0.00 2.69
167 168 2.954316 AGCGACACGTTATCACATCAA 58.046 42.857 0.00 0.00 0.00 2.57
168 169 2.647529 AGCGACACGTTATCACATCA 57.352 45.000 0.00 0.00 0.00 3.07
169 170 3.179830 AGAAGCGACACGTTATCACATC 58.820 45.455 0.00 0.00 0.00 3.06
170 171 3.232213 AGAAGCGACACGTTATCACAT 57.768 42.857 0.00 0.00 0.00 3.21
171 172 2.717580 AGAAGCGACACGTTATCACA 57.282 45.000 0.00 0.00 0.00 3.58
172 173 5.505165 TTTAAGAAGCGACACGTTATCAC 57.495 39.130 0.00 0.00 0.00 3.06
173 174 5.387649 CGTTTTAAGAAGCGACACGTTATCA 60.388 40.000 0.00 0.00 41.28 2.15
244 245 4.881850 CCTTTTCCATGTCATGTACTACCC 59.118 45.833 11.84 0.00 0.00 3.69
250 251 2.922955 TCCCCCTTTTCCATGTCATGTA 59.077 45.455 11.84 0.00 0.00 2.29
309 327 3.304458 CGATGATGTTGATGCATGGAAGG 60.304 47.826 2.46 0.00 0.00 3.46
365 384 2.711311 CACCGCTTGCATCATCGG 59.289 61.111 12.76 12.76 46.61 4.18
387 413 0.537188 ATTCAAGGAGCGACGGATGT 59.463 50.000 0.00 0.00 0.00 3.06
392 418 2.069273 AGTTGAATTCAAGGAGCGACG 58.931 47.619 21.05 0.00 36.39 5.12
405 431 6.306987 ACAAGTGGGTATGAAGAAGTTGAAT 58.693 36.000 0.00 0.00 0.00 2.57
433 459 7.819900 GGTAGTCTCTTCTTATGCTGAAAAGAA 59.180 37.037 0.00 0.00 38.93 2.52
434 460 7.179338 AGGTAGTCTCTTCTTATGCTGAAAAGA 59.821 37.037 0.00 0.00 0.00 2.52
435 461 7.327214 AGGTAGTCTCTTCTTATGCTGAAAAG 58.673 38.462 0.00 0.00 0.00 2.27
440 466 6.045955 GGAAAGGTAGTCTCTTCTTATGCTG 58.954 44.000 0.00 0.00 0.00 4.41
512 579 7.110810 TGGACGAATGTATGTTGGGTAATAAA 58.889 34.615 0.00 0.00 0.00 1.40
515 582 5.105567 TGGACGAATGTATGTTGGGTAAT 57.894 39.130 0.00 0.00 0.00 1.89
521 588 6.182039 AGAATGTTGGACGAATGTATGTTG 57.818 37.500 0.00 0.00 0.00 3.33
635 703 8.934023 AAAGTTGAGACACTTATTTTGGGATA 57.066 30.769 0.00 0.00 35.87 2.59
648 716 9.269453 ACTAAAGTTGGTATAAAGTTGAGACAC 57.731 33.333 0.00 0.00 28.96 3.67
694 762 6.940298 TCCCTTCGTCTCAAAATAAATGTCTT 59.060 34.615 0.00 0.00 0.00 3.01
695 763 6.472887 TCCCTTCGTCTCAAAATAAATGTCT 58.527 36.000 0.00 0.00 0.00 3.41
696 764 6.371825 ACTCCCTTCGTCTCAAAATAAATGTC 59.628 38.462 0.00 0.00 0.00 3.06
700 768 9.595823 CTTATACTCCCTTCGTCTCAAAATAAA 57.404 33.333 0.00 0.00 0.00 1.40
709 777 8.578151 GTGATTTATCTTATACTCCCTTCGTCT 58.422 37.037 0.00 0.00 0.00 4.18
762 830 8.948631 ACCTACTCATGTTAATGTGATTACAG 57.051 34.615 0.00 0.00 40.79 2.74
808 876 7.874940 TGCATTGCAACAGATATAAATAGTCC 58.125 34.615 9.33 0.00 34.76 3.85
822 890 4.894705 AGATAATACCCATGCATTGCAACA 59.105 37.500 16.46 0.00 43.62 3.33
827 895 6.236409 AGACAGAGATAATACCCATGCATTG 58.764 40.000 0.00 0.00 0.00 2.82
857 925 7.145474 TCTTAGGTCTAACCAAAAGGTTTCT 57.855 36.000 5.10 2.34 41.95 2.52
858 926 7.283807 TGTTCTTAGGTCTAACCAAAAGGTTTC 59.716 37.037 5.10 0.00 41.95 2.78
859 927 7.120716 TGTTCTTAGGTCTAACCAAAAGGTTT 58.879 34.615 5.10 0.00 41.95 3.27
860 928 6.665695 TGTTCTTAGGTCTAACCAAAAGGTT 58.334 36.000 5.15 5.15 41.95 3.50
861 929 6.256643 TGTTCTTAGGTCTAACCAAAAGGT 57.743 37.500 0.00 0.00 41.95 3.50
862 930 7.284716 AGTTTGTTCTTAGGTCTAACCAAAAGG 59.715 37.037 0.00 0.00 41.95 3.11
863 931 8.221965 AGTTTGTTCTTAGGTCTAACCAAAAG 57.778 34.615 0.00 2.47 41.95 2.27
864 932 9.112725 GTAGTTTGTTCTTAGGTCTAACCAAAA 57.887 33.333 0.00 0.00 41.95 2.44
865 933 8.266473 TGTAGTTTGTTCTTAGGTCTAACCAAA 58.734 33.333 0.00 0.00 41.95 3.28
866 934 7.794041 TGTAGTTTGTTCTTAGGTCTAACCAA 58.206 34.615 0.00 0.00 41.95 3.67
867 935 7.364149 TGTAGTTTGTTCTTAGGTCTAACCA 57.636 36.000 0.00 0.00 41.95 3.67
868 936 7.712205 TGTTGTAGTTTGTTCTTAGGTCTAACC 59.288 37.037 0.00 0.00 38.99 2.85
869 937 8.652810 TGTTGTAGTTTGTTCTTAGGTCTAAC 57.347 34.615 0.00 0.00 0.00 2.34
872 940 9.841295 TTTATGTTGTAGTTTGTTCTTAGGTCT 57.159 29.630 0.00 0.00 0.00 3.85
892 960 8.803235 GGGTCACTTTCTCCTTTTATTTTATGT 58.197 33.333 0.00 0.00 0.00 2.29
893 961 8.802267 TGGGTCACTTTCTCCTTTTATTTTATG 58.198 33.333 0.00 0.00 0.00 1.90
894 962 8.803235 GTGGGTCACTTTCTCCTTTTATTTTAT 58.197 33.333 0.00 0.00 0.00 1.40
895 963 8.002459 AGTGGGTCACTTTCTCCTTTTATTTTA 58.998 33.333 0.00 0.00 42.59 1.52
896 964 6.839134 AGTGGGTCACTTTCTCCTTTTATTTT 59.161 34.615 0.00 0.00 42.59 1.82
897 965 6.373759 AGTGGGTCACTTTCTCCTTTTATTT 58.626 36.000 0.00 0.00 42.59 1.40
898 966 5.953571 AGTGGGTCACTTTCTCCTTTTATT 58.046 37.500 0.00 0.00 42.59 1.40
899 967 5.584551 AGTGGGTCACTTTCTCCTTTTAT 57.415 39.130 0.00 0.00 42.59 1.40
901 969 3.953542 AGTGGGTCACTTTCTCCTTTT 57.046 42.857 0.00 0.00 42.59 2.27
912 980 4.332428 AGTACAACTACAAGTGGGTCAC 57.668 45.455 0.00 0.00 34.10 3.67
913 981 4.021719 GCTAGTACAACTACAAGTGGGTCA 60.022 45.833 0.00 0.00 0.00 4.02
914 982 4.021719 TGCTAGTACAACTACAAGTGGGTC 60.022 45.833 0.00 0.00 0.00 4.46
915 983 3.899360 TGCTAGTACAACTACAAGTGGGT 59.101 43.478 0.00 0.00 0.00 4.51
916 984 4.243270 GTGCTAGTACAACTACAAGTGGG 58.757 47.826 6.04 0.00 0.00 4.61
917 985 3.918591 CGTGCTAGTACAACTACAAGTGG 59.081 47.826 11.70 0.00 0.00 4.00
918 986 4.790878 TCGTGCTAGTACAACTACAAGTG 58.209 43.478 11.70 0.00 0.00 3.16
919 987 5.399858 CATCGTGCTAGTACAACTACAAGT 58.600 41.667 11.70 0.00 0.00 3.16
920 988 4.265556 GCATCGTGCTAGTACAACTACAAG 59.734 45.833 11.70 0.00 40.96 3.16
921 989 4.171005 GCATCGTGCTAGTACAACTACAA 58.829 43.478 11.70 0.00 40.96 2.41
922 990 3.766151 GCATCGTGCTAGTACAACTACA 58.234 45.455 11.70 0.00 40.96 2.74
972 1040 4.771356 GCGCTCGCGGACACTGTA 62.771 66.667 13.56 0.00 40.19 2.74
996 1064 3.670625 TGCAGTAGCTTTAAATGGTCGT 58.329 40.909 0.00 0.00 42.74 4.34
998 1066 5.818136 TGATGCAGTAGCTTTAAATGGTC 57.182 39.130 0.00 0.00 42.74 4.02
1075 1178 3.924686 CGCTCTAGCTCGGAACTTTTAAA 59.075 43.478 0.00 0.00 39.32 1.52
1079 1182 3.723554 CGCTCTAGCTCGGAACTTT 57.276 52.632 0.00 0.00 39.32 2.66
1086 1189 0.596083 CATGGTTCCGCTCTAGCTCG 60.596 60.000 0.00 0.00 39.32 5.03
1160 1263 2.582226 CGCGCGGCTACTCATCAA 60.582 61.111 24.84 0.00 0.00 2.57
1163 1266 4.873129 CCACGCGCGGCTACTCAT 62.873 66.667 35.22 7.19 0.00 2.90
1217 1320 2.528743 GCACGGTGATGATGCTCCG 61.529 63.158 13.29 0.00 46.93 4.63
1291 1394 1.181786 CCTGGAGCTTCTCTTCGAGT 58.818 55.000 0.00 0.00 0.00 4.18
1341 2442 5.494632 GGAGAACTCCGTTTCAAGAAAAA 57.505 39.130 5.06 0.00 40.36 1.94
1355 2456 9.507329 TGATTGCCTAAATTATATGGAGAACTC 57.493 33.333 0.00 0.00 0.00 3.01
1358 2459 8.742777 GCATGATTGCCTAAATTATATGGAGAA 58.257 33.333 0.00 0.00 43.38 2.87
1359 2460 8.284945 GCATGATTGCCTAAATTATATGGAGA 57.715 34.615 0.00 0.00 43.38 3.71
1363 2464 8.033038 AAGCAGCATGATTGCCTAAATTATATG 58.967 33.333 16.21 0.00 46.68 1.78
1413 2526 9.271828 CAACTGCTCAAACACACCATATATATA 57.728 33.333 0.00 0.00 0.00 0.86
1414 2527 7.775093 ACAACTGCTCAAACACACCATATATAT 59.225 33.333 0.00 0.00 0.00 0.86
1428 2541 0.463654 AGCCACGACAACTGCTCAAA 60.464 50.000 0.00 0.00 0.00 2.69
1443 2556 4.435436 CTCCTACGCACGCAGCCA 62.435 66.667 0.00 0.00 41.38 4.75
1446 2559 2.580867 GAGCTCCTACGCACGCAG 60.581 66.667 0.87 0.00 0.00 5.18
1683 2796 5.609088 CACTAGTTTGTATTTCTGCGTGAC 58.391 41.667 0.00 0.00 0.00 3.67
1696 2809 0.944311 CACCGCGAGCACTAGTTTGT 60.944 55.000 8.23 0.00 0.00 2.83
1698 2811 2.027625 GCACCGCGAGCACTAGTTT 61.028 57.895 8.23 0.00 0.00 2.66
1747 2860 8.458052 ACAAATGATGTGAAATGACGCTAAATA 58.542 29.630 0.00 0.00 41.93 1.40
1753 2866 4.475028 TGACAAATGATGTGAAATGACGC 58.525 39.130 0.00 0.00 44.12 5.19
1755 2868 6.097356 AGCATGACAAATGATGTGAAATGAC 58.903 36.000 0.00 0.51 44.12 3.06
1766 2879 7.105588 AGTTGACACTATAGCATGACAAATGA 58.894 34.615 0.00 0.00 33.45 2.57
1800 2913 0.240411 GCGAATAGCGACCGGAGTAT 59.760 55.000 9.46 0.00 44.57 2.12
1801 2914 1.650912 GCGAATAGCGACCGGAGTA 59.349 57.895 9.46 0.00 44.57 2.59
1831 2946 7.491696 GTGTTCACAGAGTAGTAGTTCAACTTT 59.508 37.037 0.00 0.00 0.00 2.66
1868 2983 7.625828 ACTCCCTGTGTAAACAAATATAAGC 57.374 36.000 0.00 0.00 0.00 3.09
1885 3000 3.194542 GGCAGCTAGTCATATACTCCCTG 59.805 52.174 0.00 0.00 39.80 4.45
1958 3132 0.971959 CCATAGGCCCTTTGCTGCAA 60.972 55.000 11.69 11.69 40.92 4.08
2050 3246 4.081406 TGGGAATGACAATGTTCTTGAGG 58.919 43.478 0.00 0.00 0.00 3.86
2068 3264 3.149196 GAGCTTGATGTCAAAAGTGGGA 58.851 45.455 0.00 0.00 35.15 4.37
2323 3636 4.470664 AGAAGAGCATTCTTGGAGACATCT 59.529 41.667 0.00 0.00 43.63 2.90
2375 3688 2.521224 GGGGAGATAGGTCGGCGT 60.521 66.667 6.85 0.00 0.00 5.68
2386 3699 2.938798 AAATGGTGGCCGGGGAGA 60.939 61.111 2.18 0.00 0.00 3.71
2539 3868 5.221342 GCATCACAGGAGTTAGCTAGTACAT 60.221 44.000 0.00 0.00 0.00 2.29
2554 3883 1.719709 CGCACATCAGCATCACAGG 59.280 57.895 0.00 0.00 0.00 4.00
2555 3884 1.062047 GCGCACATCAGCATCACAG 59.938 57.895 0.30 0.00 0.00 3.66
2644 3973 2.553247 GGAAGAAGTCCAGGTTTCCCAG 60.553 54.545 3.66 0.00 46.97 4.45
2732 4061 5.177511 CACTCAATTGCGTCAAACTTCTCTA 59.822 40.000 0.00 0.00 0.00 2.43
2749 4078 1.973281 CCCACTTGCCGCACTCAAT 60.973 57.895 0.00 0.00 0.00 2.57
2750 4079 2.594303 CCCACTTGCCGCACTCAA 60.594 61.111 0.00 0.00 0.00 3.02
2793 4122 3.329542 AATGATCGGCGTGGCACCT 62.330 57.895 12.86 0.00 0.00 4.00
2834 4163 0.963225 TTGGATGTCAACGAGGTCGA 59.037 50.000 6.35 0.00 43.02 4.20
2890 4219 2.158519 TGTACTGGATCCGGAGATAGCA 60.159 50.000 27.90 12.27 30.90 3.49
2911 4240 0.320771 ATTTCGCTGGTGAGCTCGTT 60.321 50.000 9.64 0.00 43.77 3.85
2923 4252 2.040544 CAACGGAGGCCATTTCGCT 61.041 57.895 5.01 0.00 0.00 4.93
3001 4330 1.537202 GTTCATCTTGCACACCTGTCC 59.463 52.381 0.00 0.00 0.00 4.02
3035 4364 3.312828 CTCTTTAGATCGGGCTCATTCG 58.687 50.000 0.00 0.00 0.00 3.34
3061 4390 0.896226 ACTAGTTCCTCCTCGTTGGC 59.104 55.000 0.00 0.00 35.26 4.52
3093 4422 0.800683 CGCGCTCTTCCGACAACATA 60.801 55.000 5.56 0.00 0.00 2.29
3114 4443 1.218316 GTAGCCCACCTTCCGAGTG 59.782 63.158 0.00 0.00 34.91 3.51
3158 4496 5.762179 AGGGTCATCAAATACAGACAGAA 57.238 39.130 0.00 0.00 32.79 3.02
3195 4537 5.122239 TGAACAAATCTCGAAAGCCACATAG 59.878 40.000 0.00 0.00 0.00 2.23
3281 4761 9.886132 ACCACGAGTATTATTTTCTTGAGTAAT 57.114 29.630 0.00 0.00 0.00 1.89
3287 4767 9.329913 CTCAAAACCACGAGTATTATTTTCTTG 57.670 33.333 0.00 0.00 0.00 3.02
3291 4771 7.360607 CGTCCTCAAAACCACGAGTATTATTTT 60.361 37.037 0.00 0.00 34.06 1.82
3294 4774 5.107133 CGTCCTCAAAACCACGAGTATTAT 58.893 41.667 0.00 0.00 34.06 1.28
3310 4790 1.305201 GAAAAGCACAACCGTCCTCA 58.695 50.000 0.00 0.00 0.00 3.86
3349 4829 4.918810 AAAGAATTTCAGGAGCGTTTGT 57.081 36.364 0.00 0.00 27.08 2.83
3350 4830 4.445385 CCAAAAGAATTTCAGGAGCGTTTG 59.555 41.667 0.00 0.00 37.28 2.93
3351 4831 4.340950 TCCAAAAGAATTTCAGGAGCGTTT 59.659 37.500 0.00 0.00 37.28 3.60
3352 4832 3.888930 TCCAAAAGAATTTCAGGAGCGTT 59.111 39.130 0.00 0.00 37.28 4.84
3353 4833 3.253432 GTCCAAAAGAATTTCAGGAGCGT 59.747 43.478 0.00 0.00 41.08 5.07
3354 4834 3.253188 TGTCCAAAAGAATTTCAGGAGCG 59.747 43.478 0.00 0.00 41.08 5.03
3355 4835 4.279420 AGTGTCCAAAAGAATTTCAGGAGC 59.721 41.667 0.00 0.00 41.08 4.70
3356 4836 6.396829 AAGTGTCCAAAAGAATTTCAGGAG 57.603 37.500 0.00 0.00 41.08 3.69
3357 4837 6.790232 AAAGTGTCCAAAAGAATTTCAGGA 57.210 33.333 0.00 0.00 37.28 3.86
3358 4838 7.014230 TCCTAAAGTGTCCAAAAGAATTTCAGG 59.986 37.037 0.00 0.00 37.28 3.86
3359 4839 7.940850 TCCTAAAGTGTCCAAAAGAATTTCAG 58.059 34.615 0.00 0.00 37.28 3.02
3361 4841 8.194769 TGTTCCTAAAGTGTCCAAAAGAATTTC 58.805 33.333 0.00 0.00 37.28 2.17
3373 4889 3.059120 GGAGCGTTTGTTCCTAAAGTGTC 60.059 47.826 0.00 0.00 41.91 3.67
3399 4915 8.056407 TCCGGTTTCCAAAAATTTCAAAAATT 57.944 26.923 0.00 0.00 0.00 1.82
3406 4923 7.351981 CAGAAAATCCGGTTTCCAAAAATTTC 58.648 34.615 12.58 4.49 38.10 2.17
3411 4928 3.493524 GCCAGAAAATCCGGTTTCCAAAA 60.494 43.478 12.58 0.00 38.10 2.44
3419 4936 0.917333 TAGGGGCCAGAAAATCCGGT 60.917 55.000 4.39 0.00 0.00 5.28
3421 4938 0.465642 GGTAGGGGCCAGAAAATCCG 60.466 60.000 4.39 0.00 0.00 4.18
3422 4939 0.629058 TGGTAGGGGCCAGAAAATCC 59.371 55.000 4.39 0.00 33.97 3.01
3462 4979 7.117667 GCCGAATCAACCTATTTGTTTCAAAAT 59.882 33.333 7.99 0.00 41.30 1.82
3471 4988 1.333619 CGGGCCGAATCAACCTATTTG 59.666 52.381 24.41 0.00 36.42 2.32
3494 5011 5.067674 AGCTCACACAAAAGCATGACTAAAA 59.932 36.000 0.00 0.00 41.06 1.52
3505 5022 1.331756 AGTCGCAAGCTCACACAAAAG 59.668 47.619 0.00 0.00 37.18 2.27
3519 5259 4.550422 GCATGAGTCTTATCATAGTCGCA 58.450 43.478 0.00 0.00 37.84 5.10
3525 5265 6.324770 TCAACTCTGGCATGAGTCTTATCATA 59.675 38.462 16.37 0.07 45.49 2.15
3538 5278 1.072806 TCACAAGCTCAACTCTGGCAT 59.927 47.619 0.00 0.00 0.00 4.40
3541 5281 3.265791 GGTATCACAAGCTCAACTCTGG 58.734 50.000 0.00 0.00 0.00 3.86
3547 5287 4.227300 AGGGTATTGGTATCACAAGCTCAA 59.773 41.667 0.00 0.00 33.23 3.02
3548 5288 3.780294 AGGGTATTGGTATCACAAGCTCA 59.220 43.478 0.00 0.00 33.23 4.26
3551 5291 4.423625 AGAGGGTATTGGTATCACAAGC 57.576 45.455 0.00 0.00 33.23 4.01
3552 5292 7.735917 TGAATAGAGGGTATTGGTATCACAAG 58.264 38.462 0.00 0.00 33.23 3.16
3553 5293 7.684317 TGAATAGAGGGTATTGGTATCACAA 57.316 36.000 0.00 0.00 34.41 3.33
3575 5315 2.224018 GCATCACCAAAAAGGCAGTTGA 60.224 45.455 0.00 0.00 43.14 3.18
3582 5651 5.957842 TGTAAGTAGCATCACCAAAAAGG 57.042 39.130 0.00 0.00 45.67 3.11
3593 5662 5.765182 GGCAGTTGGATATTGTAAGTAGCAT 59.235 40.000 0.00 0.00 0.00 3.79
3597 5666 8.644374 AAAAAGGCAGTTGGATATTGTAAGTA 57.356 30.769 0.00 0.00 0.00 2.24
3658 5727 6.094186 GGAAATTGAGTCCACAAATAGGTCTC 59.906 42.308 0.00 0.00 40.35 3.36
3671 5740 3.314080 TCAAACACACGGAAATTGAGTCC 59.686 43.478 0.00 0.00 0.00 3.85
3684 5753 7.096640 CGGAAACAGTGAAATAATCAAACACAC 60.097 37.037 0.00 0.00 40.50 3.82
3718 5788 7.255346 GGTTAGTTAAGTTGCTTGGTGTTACAT 60.255 37.037 0.00 0.00 0.00 2.29
3719 5789 6.038492 GGTTAGTTAAGTTGCTTGGTGTTACA 59.962 38.462 0.00 0.00 0.00 2.41
3739 5809 9.487790 AAAACCAACACATTTTATCATGGTTAG 57.512 29.630 7.62 0.00 46.01 2.34
3754 5824 6.588204 AGTACATAGACTCAAAACCAACACA 58.412 36.000 0.00 0.00 0.00 3.72
3764 5834 8.675504 GTGCTAGAAACTAGTACATAGACTCAA 58.324 37.037 17.37 0.00 35.30 3.02
3766 5836 8.124199 GTGTGCTAGAAACTAGTACATAGACTC 58.876 40.741 23.93 12.18 41.00 3.36
3773 5843 5.777850 TGTGTGTGCTAGAAACTAGTACA 57.222 39.130 19.78 19.78 37.72 2.90
3774 5844 7.384115 TCAATTGTGTGTGCTAGAAACTAGTAC 59.616 37.037 16.09 16.09 0.00 2.73
3794 5986 6.096695 TGATCTCACATGCACAATTCAATTG 58.903 36.000 8.67 8.67 45.59 2.32
3851 6043 6.208644 GTTTTGTTTTGCAAGATCAGCTCTA 58.791 36.000 10.87 0.00 38.47 2.43
3879 6071 4.040461 TCATAGCAGTATAGGGCCAAAGAC 59.960 45.833 6.18 0.11 0.00 3.01
3885 6077 4.625607 ACTTTCATAGCAGTATAGGGCC 57.374 45.455 0.00 0.00 0.00 5.80
3952 6146 6.942576 AGGATGGTTATGCTGGAATACAATAC 59.057 38.462 0.00 0.00 33.29 1.89
3976 6170 5.220815 CGTAAGTAGTACTCAAGGTGCCTAG 60.221 48.000 2.58 0.00 0.00 3.02
3998 6192 1.003233 AGGAAAAGAAGGCGGAATCGT 59.997 47.619 0.00 0.00 38.89 3.73
3999 6193 1.666189 GAGGAAAAGAAGGCGGAATCG 59.334 52.381 0.00 0.00 39.81 3.34
4140 9188 3.071312 TGCCCTTGTTTGAATTTGATGCT 59.929 39.130 0.00 0.00 0.00 3.79
4141 9189 3.401182 TGCCCTTGTTTGAATTTGATGC 58.599 40.909 0.00 0.00 0.00 3.91
4157 9205 5.598417 GGTGGATAGTTTGAATATTTGCCCT 59.402 40.000 0.00 0.00 0.00 5.19
4236 9284 2.975799 GAACTGGCCCGTTTCGCA 60.976 61.111 14.25 0.00 0.00 5.10
4259 9307 4.324254 CCAATCTAAAGAGGGGCACTAACA 60.324 45.833 0.00 0.00 0.00 2.41
4322 9370 0.247736 CGAGGTGCTGCTAAAGAGGT 59.752 55.000 0.00 0.00 0.00 3.85
4336 9384 0.957395 CTCATTGCTGTTGGCGAGGT 60.957 55.000 0.00 0.00 45.43 3.85
4344 9392 0.537143 TCAACGGGCTCATTGCTGTT 60.537 50.000 0.00 0.00 42.39 3.16
4348 9396 1.675641 ACCTCAACGGGCTCATTGC 60.676 57.895 0.00 0.00 41.94 3.56
4455 9503 0.106708 AGGCGTCTGTGCTCTTTCAA 59.893 50.000 0.00 0.00 34.52 2.69


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

AutoCloner maintained by Alex Coulton.