Multiple sequence alignment - TraesCS5D01G216500

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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 TraesCS5D01G216500 chr5D 100.000 3582 0 0 1 3582 325645822 325649403 0.000000e+00 6615.0
1 TraesCS5D01G216500 chr5D 88.310 941 69 27 728 1647 325663374 325664294 0.000000e+00 1090.0
2 TraesCS5D01G216500 chr5D 89.817 766 68 7 2283 3045 326119651 326120409 0.000000e+00 974.0
3 TraesCS5D01G216500 chr5D 97.601 542 12 1 3042 3582 103097021 103097562 0.000000e+00 928.0
4 TraesCS5D01G216500 chr5D 97.422 543 11 3 3042 3582 527641535 527640994 0.000000e+00 922.0
5 TraesCS5D01G216500 chr5D 97.417 542 10 4 3043 3582 518720486 518721025 0.000000e+00 920.0
6 TraesCS5D01G216500 chr5D 91.437 654 41 3 2393 3045 325664877 325665516 0.000000e+00 883.0
7 TraesCS5D01G216500 chr5D 86.892 740 67 19 937 1647 326118041 326118779 0.000000e+00 802.0
8 TraesCS5D01G216500 chr5D 82.710 642 75 22 1001 1633 325422710 325423324 4.070000e-149 538.0
9 TraesCS5D01G216500 chr5D 87.955 440 36 9 1647 2071 325664390 325664827 1.480000e-138 503.0
10 TraesCS5D01G216500 chr5D 86.005 443 51 9 1789 2228 326119094 326119528 7.000000e-127 464.0
11 TraesCS5D01G216500 chr5D 86.415 265 20 8 389 649 325663067 325663319 3.520000e-70 276.0
12 TraesCS5D01G216500 chr5D 84.375 160 22 3 2 159 325902061 325902219 1.720000e-33 154.0
13 TraesCS5D01G216500 chr5D 97.619 42 1 0 845 886 326117906 326117947 4.960000e-09 73.1
14 TraesCS5D01G216500 chr5A 87.266 1547 112 38 728 2230 430958874 430957369 0.000000e+00 1687.0
15 TraesCS5D01G216500 chr5A 90.965 819 65 4 2231 3045 430957333 430956520 0.000000e+00 1094.0
16 TraesCS5D01G216500 chr5A 94.190 654 35 2 2393 3045 431029495 431028844 0.000000e+00 994.0
17 TraesCS5D01G216500 chr5A 90.196 765 65 7 2284 3045 430506927 430506170 0.000000e+00 989.0
18 TraesCS5D01G216500 chr5A 85.443 948 74 22 728 1615 431045404 431044461 0.000000e+00 928.0
19 TraesCS5D01G216500 chr5A 88.493 730 64 16 936 1650 430508522 430507798 0.000000e+00 865.0
20 TraesCS5D01G216500 chr5A 86.395 441 40 11 1647 2071 431029978 431029542 7.000000e-127 464.0
21 TraesCS5D01G216500 chr5A 85.618 445 53 7 1789 2228 430507492 430507054 1.170000e-124 457.0
22 TraesCS5D01G216500 chr5A 85.714 266 23 5 388 649 430959182 430958928 2.120000e-67 267.0
23 TraesCS5D01G216500 chr5A 83.482 224 33 3 1801 2022 423681174 423681395 4.690000e-49 206.0
24 TraesCS5D01G216500 chr5A 81.154 260 23 9 391 649 431045693 431045459 6.110000e-43 185.0
25 TraesCS5D01G216500 chr5A 88.095 126 9 4 1647 1769 430507674 430507552 1.040000e-30 145.0
26 TraesCS5D01G216500 chr5A 81.818 88 10 3 845 931 430508660 430508578 6.420000e-08 69.4
27 TraesCS5D01G216500 chr5B 92.901 817 53 4 2231 3045 378069760 378070573 0.000000e+00 1182.0
28 TraesCS5D01G216500 chr5B 87.397 968 57 32 728 1634 378068012 378068975 0.000000e+00 1051.0
29 TraesCS5D01G216500 chr5B 86.475 976 70 26 730 1650 377977898 377978866 0.000000e+00 1014.0
30 TraesCS5D01G216500 chr5B 89.777 763 66 7 2287 3045 378512095 378512849 0.000000e+00 966.0
31 TraesCS5D01G216500 chr5B 92.078 669 51 1 2377 3045 377979603 377980269 0.000000e+00 941.0
32 TraesCS5D01G216500 chr5B 89.148 728 58 16 936 1647 378510497 378511219 0.000000e+00 887.0
33 TraesCS5D01G216500 chr5B 88.075 587 46 10 1664 2230 378069142 378069724 0.000000e+00 675.0
34 TraesCS5D01G216500 chr5B 85.502 607 59 14 1640 2227 377978963 377979559 1.100000e-169 606.0
35 TraesCS5D01G216500 chr5B 85.393 445 54 7 1789 2228 378511531 378511969 5.450000e-123 451.0
36 TraesCS5D01G216500 chr5B 90.265 226 17 4 395 620 377976193 377976413 1.260000e-74 291.0
37 TraesCS5D01G216500 chr5B 86.066 244 25 8 406 646 378509981 378510218 1.650000e-63 254.0
38 TraesCS5D01G216500 chr5B 84.586 266 18 9 388 649 378067711 378067957 3.570000e-60 243.0
39 TraesCS5D01G216500 chr5B 93.590 156 9 1 230 384 377974740 377974895 7.730000e-57 231.0
40 TraesCS5D01G216500 chr5B 87.302 126 10 4 1647 1769 378511349 378511471 4.820000e-29 139.0
41 TraesCS5D01G216500 chr5B 83.117 77 7 3 845 920 378510363 378510434 8.300000e-07 65.8
42 TraesCS5D01G216500 chr4D 97.601 542 12 1 3042 3582 105474884 105474343 0.000000e+00 928.0
43 TraesCS5D01G216500 chr4D 97.597 541 11 2 3043 3582 453403152 453402613 0.000000e+00 926.0
44 TraesCS5D01G216500 chr4D 97.417 542 12 2 3042 3582 105467650 105467110 0.000000e+00 922.0
45 TraesCS5D01G216500 chr7D 97.422 543 12 2 3041 3582 533129102 533129643 0.000000e+00 924.0
46 TraesCS5D01G216500 chr3D 97.417 542 12 2 3042 3582 362082581 362082041 0.000000e+00 922.0
47 TraesCS5D01G216500 chr6D 97.232 542 13 2 3042 3582 170979886 170980426 0.000000e+00 917.0
48 TraesCS5D01G216500 chr7A 80.191 419 65 11 1811 2228 22039419 22039820 7.520000e-77 298.0
49 TraesCS5D01G216500 chr7A 79.475 419 68 11 1811 2228 21616904 21617305 7.570000e-72 281.0
50 TraesCS5D01G216500 chrUn 84.722 144 21 1 1789 1932 311754838 311754980 3.730000e-30 143.0
51 TraesCS5D01G216500 chrUn 84.722 144 21 1 1789 1932 353102493 353102635 3.730000e-30 143.0
52 TraesCS5D01G216500 chr4A 89.412 85 5 4 151 233 704532434 704532516 1.760000e-18 104.0


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 TraesCS5D01G216500 chr5D 325645822 325649403 3581 False 6615.000000 6615 100.000000 1 3582 1 chr5D.!!$F3 3581
1 TraesCS5D01G216500 chr5D 103097021 103097562 541 False 928.000000 928 97.601000 3042 3582 1 chr5D.!!$F1 540
2 TraesCS5D01G216500 chr5D 527640994 527641535 541 True 922.000000 922 97.422000 3042 3582 1 chr5D.!!$R1 540
3 TraesCS5D01G216500 chr5D 518720486 518721025 539 False 920.000000 920 97.417000 3043 3582 1 chr5D.!!$F5 539
4 TraesCS5D01G216500 chr5D 325663067 325665516 2449 False 688.000000 1090 88.529250 389 3045 4 chr5D.!!$F6 2656
5 TraesCS5D01G216500 chr5D 326117906 326120409 2503 False 578.275000 974 90.083250 845 3045 4 chr5D.!!$F7 2200
6 TraesCS5D01G216500 chr5D 325422710 325423324 614 False 538.000000 538 82.710000 1001 1633 1 chr5D.!!$F2 632
7 TraesCS5D01G216500 chr5A 430956520 430959182 2662 True 1016.000000 1687 87.981667 388 3045 3 chr5A.!!$R2 2657
8 TraesCS5D01G216500 chr5A 431028844 431029978 1134 True 729.000000 994 90.292500 1647 3045 2 chr5A.!!$R3 1398
9 TraesCS5D01G216500 chr5A 431044461 431045693 1232 True 556.500000 928 83.298500 391 1615 2 chr5A.!!$R4 1224
10 TraesCS5D01G216500 chr5A 430506170 430508660 2490 True 505.080000 989 86.844000 845 3045 5 chr5A.!!$R1 2200
11 TraesCS5D01G216500 chr5B 378067711 378070573 2862 False 787.750000 1182 88.239750 388 3045 4 chr5B.!!$F2 2657
12 TraesCS5D01G216500 chr5B 377974740 377980269 5529 False 616.600000 1014 89.582000 230 3045 5 chr5B.!!$F1 2815
13 TraesCS5D01G216500 chr5B 378509981 378512849 2868 False 460.466667 966 86.800500 406 3045 6 chr5B.!!$F3 2639
14 TraesCS5D01G216500 chr4D 105474343 105474884 541 True 928.000000 928 97.601000 3042 3582 1 chr4D.!!$R2 540
15 TraesCS5D01G216500 chr4D 453402613 453403152 539 True 926.000000 926 97.597000 3043 3582 1 chr4D.!!$R3 539
16 TraesCS5D01G216500 chr4D 105467110 105467650 540 True 922.000000 922 97.417000 3042 3582 1 chr4D.!!$R1 540
17 TraesCS5D01G216500 chr7D 533129102 533129643 541 False 924.000000 924 97.422000 3041 3582 1 chr7D.!!$F1 541
18 TraesCS5D01G216500 chr3D 362082041 362082581 540 True 922.000000 922 97.417000 3042 3582 1 chr3D.!!$R1 540
19 TraesCS5D01G216500 chr6D 170979886 170980426 540 False 917.000000 917 97.232000 3042 3582 1 chr6D.!!$F1 540

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
201 202 0.035630 AGCTTAGTTGAGGCCTGCAG 60.036 55.0 12.00 6.78 0.00 4.41 F
380 382 0.178975 TTTGACCGGGCAATCACCTT 60.179 50.0 26.67 0.00 0.00 3.50 F
1464 4391 0.185901 TTTCCAAGCCTGGCTGACTT 59.814 50.0 24.16 2.75 43.17 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 4959 1.162698 CTCCACGTCGACCAAGAGTA 58.837 55.000 10.58 0.0 0.00 2.59 R
1956 5112 1.207329 GAGGCCTTGAAGTCACGGTAT 59.793 52.381 6.77 0.0 37.56 2.73 R
2814 6051 1.154430 TGGGCCTAGACTTTGGGTTT 58.846 50.000 4.53 0.0 0.00 3.27 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
19 20 0.588252 ATAGCGGATTCGTGCAATGC 59.412 50.000 0.00 0.00 38.89 3.56
20 21 0.461870 TAGCGGATTCGTGCAATGCT 60.462 50.000 6.82 0.00 38.89 3.79
21 22 1.137404 GCGGATTCGTGCAATGCTT 59.863 52.632 6.82 0.00 38.89 3.91
22 23 0.376852 GCGGATTCGTGCAATGCTTA 59.623 50.000 6.82 0.00 38.89 3.09
23 24 1.202132 GCGGATTCGTGCAATGCTTAA 60.202 47.619 6.82 0.00 38.89 1.85
24 25 2.708514 CGGATTCGTGCAATGCTTAAG 58.291 47.619 6.82 0.00 30.62 1.85
25 26 2.351418 CGGATTCGTGCAATGCTTAAGA 59.649 45.455 6.67 0.00 30.62 2.10
26 27 3.002656 CGGATTCGTGCAATGCTTAAGAT 59.997 43.478 6.67 0.00 30.62 2.40
27 28 4.285292 GGATTCGTGCAATGCTTAAGATG 58.715 43.478 6.67 2.90 30.18 2.90
28 29 3.763097 TTCGTGCAATGCTTAAGATGG 57.237 42.857 6.67 0.00 0.00 3.51
29 30 2.710377 TCGTGCAATGCTTAAGATGGT 58.290 42.857 6.67 0.00 0.00 3.55
30 31 3.081061 TCGTGCAATGCTTAAGATGGTT 58.919 40.909 6.67 0.00 0.00 3.67
31 32 3.119884 TCGTGCAATGCTTAAGATGGTTG 60.120 43.478 6.67 6.01 0.00 3.77
32 33 3.366273 CGTGCAATGCTTAAGATGGTTGT 60.366 43.478 6.67 0.00 0.00 3.32
33 34 4.559153 GTGCAATGCTTAAGATGGTTGTT 58.441 39.130 6.67 0.00 0.00 2.83
34 35 4.990426 GTGCAATGCTTAAGATGGTTGTTT 59.010 37.500 6.67 0.00 0.00 2.83
35 36 6.155827 GTGCAATGCTTAAGATGGTTGTTTA 58.844 36.000 6.67 0.00 0.00 2.01
36 37 6.813152 GTGCAATGCTTAAGATGGTTGTTTAT 59.187 34.615 6.67 0.00 0.00 1.40
37 38 7.331687 GTGCAATGCTTAAGATGGTTGTTTATT 59.668 33.333 6.67 0.00 0.00 1.40
38 39 7.545265 TGCAATGCTTAAGATGGTTGTTTATTC 59.455 33.333 6.67 0.00 0.00 1.75
39 40 7.010460 GCAATGCTTAAGATGGTTGTTTATTCC 59.990 37.037 6.67 0.00 0.00 3.01
40 41 6.524101 TGCTTAAGATGGTTGTTTATTCCC 57.476 37.500 6.67 0.00 0.00 3.97
41 42 5.124776 TGCTTAAGATGGTTGTTTATTCCCG 59.875 40.000 6.67 0.00 0.00 5.14
42 43 5.355910 GCTTAAGATGGTTGTTTATTCCCGA 59.644 40.000 6.67 0.00 0.00 5.14
43 44 6.127842 GCTTAAGATGGTTGTTTATTCCCGAA 60.128 38.462 6.67 0.00 0.00 4.30
44 45 7.576098 GCTTAAGATGGTTGTTTATTCCCGAAA 60.576 37.037 6.67 0.00 0.00 3.46
45 46 5.638596 AGATGGTTGTTTATTCCCGAAAC 57.361 39.130 0.00 0.00 37.32 2.78
46 47 3.900388 TGGTTGTTTATTCCCGAAACG 57.100 42.857 0.00 0.00 39.23 3.60
47 48 2.030981 TGGTTGTTTATTCCCGAAACGC 60.031 45.455 0.00 0.00 39.23 4.84
48 49 2.227149 GGTTGTTTATTCCCGAAACGCT 59.773 45.455 0.00 0.00 39.23 5.07
49 50 3.436359 GGTTGTTTATTCCCGAAACGCTA 59.564 43.478 0.00 0.00 39.23 4.26
50 51 4.095334 GGTTGTTTATTCCCGAAACGCTAT 59.905 41.667 0.00 0.00 39.23 2.97
51 52 5.392272 GGTTGTTTATTCCCGAAACGCTATT 60.392 40.000 0.00 0.00 39.23 1.73
52 53 6.183360 GGTTGTTTATTCCCGAAACGCTATTA 60.183 38.462 0.00 0.00 39.23 0.98
53 54 7.412063 GTTGTTTATTCCCGAAACGCTATTAT 58.588 34.615 0.00 0.00 39.23 1.28
54 55 7.556733 TGTTTATTCCCGAAACGCTATTATT 57.443 32.000 0.00 0.00 39.23 1.40
55 56 7.987649 TGTTTATTCCCGAAACGCTATTATTT 58.012 30.769 0.00 0.00 39.23 1.40
56 57 8.460428 TGTTTATTCCCGAAACGCTATTATTTT 58.540 29.630 0.00 0.00 39.23 1.82
57 58 8.950961 GTTTATTCCCGAAACGCTATTATTTTC 58.049 33.333 0.00 0.00 0.00 2.29
58 59 5.488645 TTCCCGAAACGCTATTATTTTCC 57.511 39.130 0.00 0.00 0.00 3.13
59 60 4.773013 TCCCGAAACGCTATTATTTTCCT 58.227 39.130 0.00 0.00 0.00 3.36
60 61 5.187687 TCCCGAAACGCTATTATTTTCCTT 58.812 37.500 0.00 0.00 0.00 3.36
61 62 6.347696 TCCCGAAACGCTATTATTTTCCTTA 58.652 36.000 0.00 0.00 0.00 2.69
62 63 6.993902 TCCCGAAACGCTATTATTTTCCTTAT 59.006 34.615 0.00 0.00 0.00 1.73
63 64 7.499895 TCCCGAAACGCTATTATTTTCCTTATT 59.500 33.333 0.00 0.00 0.00 1.40
64 65 7.589954 CCCGAAACGCTATTATTTTCCTTATTG 59.410 37.037 0.00 0.00 0.00 1.90
65 66 8.126700 CCGAAACGCTATTATTTTCCTTATTGT 58.873 33.333 0.00 0.00 0.00 2.71
66 67 8.943925 CGAAACGCTATTATTTTCCTTATTGTG 58.056 33.333 0.00 0.00 0.00 3.33
67 68 9.783256 GAAACGCTATTATTTTCCTTATTGTGT 57.217 29.630 0.00 0.00 0.00 3.72
97 98 7.603297 AGTTACGAAATTCATTTTTGTGTCG 57.397 32.000 0.00 0.00 41.21 4.35
98 99 6.635239 AGTTACGAAATTCATTTTTGTGTCGG 59.365 34.615 0.00 0.00 41.21 4.79
99 100 4.927422 ACGAAATTCATTTTTGTGTCGGT 58.073 34.783 0.00 0.00 39.90 4.69
100 101 4.973663 ACGAAATTCATTTTTGTGTCGGTC 59.026 37.500 0.00 0.00 39.90 4.79
101 102 5.212194 CGAAATTCATTTTTGTGTCGGTCT 58.788 37.500 0.00 0.00 0.00 3.85
102 103 6.017770 ACGAAATTCATTTTTGTGTCGGTCTA 60.018 34.615 0.00 0.00 39.90 2.59
103 104 6.302313 CGAAATTCATTTTTGTGTCGGTCTAC 59.698 38.462 0.00 0.00 0.00 2.59
104 105 6.627395 AATTCATTTTTGTGTCGGTCTACA 57.373 33.333 0.00 0.00 0.00 2.74
138 139 6.882610 TGTATCCTAATTATGCAAAGGCTG 57.117 37.500 0.00 0.00 41.91 4.85
139 140 5.769662 TGTATCCTAATTATGCAAAGGCTGG 59.230 40.000 0.00 0.00 41.91 4.85
140 141 3.565307 TCCTAATTATGCAAAGGCTGGG 58.435 45.455 0.00 0.00 41.91 4.45
141 142 3.052944 TCCTAATTATGCAAAGGCTGGGT 60.053 43.478 0.00 0.00 41.91 4.51
142 143 3.068590 CCTAATTATGCAAAGGCTGGGTG 59.931 47.826 0.00 0.00 41.91 4.61
143 144 2.236489 ATTATGCAAAGGCTGGGTGT 57.764 45.000 0.00 0.00 41.91 4.16
144 145 1.255882 TTATGCAAAGGCTGGGTGTG 58.744 50.000 0.00 0.00 41.91 3.82
145 146 0.403655 TATGCAAAGGCTGGGTGTGA 59.596 50.000 0.00 0.00 41.91 3.58
146 147 1.181098 ATGCAAAGGCTGGGTGTGAC 61.181 55.000 0.00 0.00 41.91 3.67
147 148 1.529244 GCAAAGGCTGGGTGTGACT 60.529 57.895 0.00 0.00 36.96 3.41
148 149 1.518903 GCAAAGGCTGGGTGTGACTC 61.519 60.000 0.00 0.00 36.96 3.36
149 150 0.179020 CAAAGGCTGGGTGTGACTCA 60.179 55.000 0.00 0.00 0.00 3.41
150 151 0.773644 AAAGGCTGGGTGTGACTCAT 59.226 50.000 0.00 0.00 0.00 2.90
151 152 1.656587 AAGGCTGGGTGTGACTCATA 58.343 50.000 0.00 0.00 0.00 2.15
152 153 1.656587 AGGCTGGGTGTGACTCATAA 58.343 50.000 0.00 0.00 0.00 1.90
153 154 2.200081 AGGCTGGGTGTGACTCATAAT 58.800 47.619 0.00 0.00 0.00 1.28
154 155 3.384168 AGGCTGGGTGTGACTCATAATA 58.616 45.455 0.00 0.00 0.00 0.98
155 156 3.976654 AGGCTGGGTGTGACTCATAATAT 59.023 43.478 0.00 0.00 0.00 1.28
156 157 4.413520 AGGCTGGGTGTGACTCATAATATT 59.586 41.667 0.00 0.00 0.00 1.28
157 158 5.103940 AGGCTGGGTGTGACTCATAATATTT 60.104 40.000 0.00 0.00 0.00 1.40
158 159 5.594317 GGCTGGGTGTGACTCATAATATTTT 59.406 40.000 0.00 0.00 0.00 1.82
159 160 6.770785 GGCTGGGTGTGACTCATAATATTTTA 59.229 38.462 0.00 0.00 0.00 1.52
160 161 7.284489 GGCTGGGTGTGACTCATAATATTTTAA 59.716 37.037 0.00 0.00 0.00 1.52
161 162 8.345565 GCTGGGTGTGACTCATAATATTTTAAG 58.654 37.037 0.00 0.00 0.00 1.85
162 163 9.613428 CTGGGTGTGACTCATAATATTTTAAGA 57.387 33.333 0.00 0.00 0.00 2.10
179 180 8.975410 ATTTTAAGATAGTAAAAACCAACGGC 57.025 30.769 0.00 0.00 36.73 5.68
180 181 4.673534 AAGATAGTAAAAACCAACGGCG 57.326 40.909 4.80 4.80 0.00 6.46
181 182 3.004862 AGATAGTAAAAACCAACGGCGG 58.995 45.455 13.24 0.00 0.00 6.13
182 183 2.540265 TAGTAAAAACCAACGGCGGA 57.460 45.000 13.24 0.00 0.00 5.54
183 184 1.232119 AGTAAAAACCAACGGCGGAG 58.768 50.000 13.24 2.29 0.00 4.63
196 197 4.522971 CGGAGCTTAGTTGAGGCC 57.477 61.111 0.00 0.00 0.00 5.19
197 198 1.901085 CGGAGCTTAGTTGAGGCCT 59.099 57.895 3.86 3.86 0.00 5.19
198 199 0.460987 CGGAGCTTAGTTGAGGCCTG 60.461 60.000 12.00 0.00 0.00 4.85
199 200 0.746204 GGAGCTTAGTTGAGGCCTGC 60.746 60.000 12.00 5.15 0.00 4.85
200 201 0.036010 GAGCTTAGTTGAGGCCTGCA 60.036 55.000 12.00 5.19 0.00 4.41
201 202 0.035630 AGCTTAGTTGAGGCCTGCAG 60.036 55.000 12.00 6.78 0.00 4.41
202 203 1.028868 GCTTAGTTGAGGCCTGCAGG 61.029 60.000 29.34 29.34 38.53 4.85
203 204 0.393537 CTTAGTTGAGGCCTGCAGGG 60.394 60.000 33.46 15.81 35.18 4.45
204 205 1.852157 TTAGTTGAGGCCTGCAGGGG 61.852 60.000 33.46 11.62 35.18 4.79
221 222 3.825623 GCCATGGCCCCCTAGCTT 61.826 66.667 27.24 0.00 34.56 3.74
222 223 3.018901 CCATGGCCCCCTAGCTTT 58.981 61.111 0.00 0.00 0.00 3.51
223 224 2.006805 GCCATGGCCCCCTAGCTTTA 62.007 60.000 27.24 0.00 34.56 1.85
224 225 0.178990 CCATGGCCCCCTAGCTTTAC 60.179 60.000 0.00 0.00 0.00 2.01
225 226 0.846693 CATGGCCCCCTAGCTTTACT 59.153 55.000 0.00 0.00 0.00 2.24
226 227 2.054799 CATGGCCCCCTAGCTTTACTA 58.945 52.381 0.00 0.00 0.00 1.82
227 228 1.503800 TGGCCCCCTAGCTTTACTAC 58.496 55.000 0.00 0.00 0.00 2.73
228 229 1.273953 TGGCCCCCTAGCTTTACTACA 60.274 52.381 0.00 0.00 0.00 2.74
234 235 3.937079 CCCCTAGCTTTACTACAAAACGG 59.063 47.826 0.00 0.00 0.00 4.44
270 271 6.923012 TCCGTACTGCATACAAAAGTAGTAA 58.077 36.000 0.00 0.00 35.29 2.24
273 274 7.201410 CCGTACTGCATACAAAAGTAGTAAGTG 60.201 40.741 0.00 0.00 35.29 3.16
301 302 8.690680 ATAGACAGTAAAGAAAGTAAGCGAAG 57.309 34.615 0.00 0.00 0.00 3.79
371 373 4.865925 GGTAACAAATAATTTTGACCGGGC 59.134 41.667 6.32 1.57 44.11 6.13
380 382 0.178975 TTTGACCGGGCAATCACCTT 60.179 50.000 26.67 0.00 0.00 3.50
441 1730 2.902705 AGCAGAAAACCACGTCTACA 57.097 45.000 0.00 0.00 0.00 2.74
446 1735 4.437659 GCAGAAAACCACGTCTACAAAACA 60.438 41.667 0.00 0.00 0.00 2.83
564 1872 3.674682 GCGGCTGATCTGATCTGGTATAC 60.675 52.174 21.28 8.09 0.00 1.47
653 3372 4.564372 AGTCAACTCAATCGAACATCATCG 59.436 41.667 0.00 0.00 44.04 3.84
656 3375 2.159043 ACTCAATCGAACATCATCGGCT 60.159 45.455 0.00 0.00 42.92 5.52
657 3376 2.204237 TCAATCGAACATCATCGGCTG 58.796 47.619 0.00 0.00 42.92 4.85
658 3377 1.935873 CAATCGAACATCATCGGCTGT 59.064 47.619 0.00 0.00 42.92 4.40
659 3378 2.315925 ATCGAACATCATCGGCTGTT 57.684 45.000 0.00 0.00 42.92 3.16
660 3379 2.093306 TCGAACATCATCGGCTGTTT 57.907 45.000 0.00 0.00 42.92 2.83
661 3380 1.999735 TCGAACATCATCGGCTGTTTC 59.000 47.619 0.00 0.00 42.92 2.78
662 3381 1.731709 CGAACATCATCGGCTGTTTCA 59.268 47.619 0.00 0.00 39.12 2.69
663 3382 2.474526 CGAACATCATCGGCTGTTTCAC 60.475 50.000 0.00 0.00 39.12 3.18
664 3383 2.479566 ACATCATCGGCTGTTTCACT 57.520 45.000 0.00 0.00 0.00 3.41
665 3384 2.783135 ACATCATCGGCTGTTTCACTT 58.217 42.857 0.00 0.00 0.00 3.16
666 3385 3.937814 ACATCATCGGCTGTTTCACTTA 58.062 40.909 0.00 0.00 0.00 2.24
667 3386 3.684788 ACATCATCGGCTGTTTCACTTAC 59.315 43.478 0.00 0.00 0.00 2.34
668 3387 3.678056 TCATCGGCTGTTTCACTTACT 57.322 42.857 0.00 0.00 0.00 2.24
669 3388 4.002906 TCATCGGCTGTTTCACTTACTT 57.997 40.909 0.00 0.00 0.00 2.24
670 3389 4.385825 TCATCGGCTGTTTCACTTACTTT 58.614 39.130 0.00 0.00 0.00 2.66
671 3390 4.819630 TCATCGGCTGTTTCACTTACTTTT 59.180 37.500 0.00 0.00 0.00 2.27
672 3391 5.298276 TCATCGGCTGTTTCACTTACTTTTT 59.702 36.000 0.00 0.00 0.00 1.94
673 3392 4.915704 TCGGCTGTTTCACTTACTTTTTG 58.084 39.130 0.00 0.00 0.00 2.44
674 3393 4.041723 CGGCTGTTTCACTTACTTTTTGG 58.958 43.478 0.00 0.00 0.00 3.28
675 3394 4.201970 CGGCTGTTTCACTTACTTTTTGGA 60.202 41.667 0.00 0.00 0.00 3.53
676 3395 5.281727 GGCTGTTTCACTTACTTTTTGGAG 58.718 41.667 0.00 0.00 0.00 3.86
677 3396 5.281727 GCTGTTTCACTTACTTTTTGGAGG 58.718 41.667 0.00 0.00 0.00 4.30
678 3397 5.736207 GCTGTTTCACTTACTTTTTGGAGGG 60.736 44.000 0.00 0.00 0.00 4.30
679 3398 5.511363 TGTTTCACTTACTTTTTGGAGGGA 58.489 37.500 0.00 0.00 0.00 4.20
680 3399 5.592688 TGTTTCACTTACTTTTTGGAGGGAG 59.407 40.000 0.00 0.00 0.00 4.30
681 3400 4.367039 TCACTTACTTTTTGGAGGGAGG 57.633 45.455 0.00 0.00 0.00 4.30
682 3401 3.073946 TCACTTACTTTTTGGAGGGAGGG 59.926 47.826 0.00 0.00 0.00 4.30
683 3402 2.378886 ACTTACTTTTTGGAGGGAGGGG 59.621 50.000 0.00 0.00 0.00 4.79
684 3403 0.702316 TACTTTTTGGAGGGAGGGGC 59.298 55.000 0.00 0.00 0.00 5.80
699 3418 3.866356 GGCAACCTACGTCGTTCC 58.134 61.111 1.78 0.00 0.00 3.62
702 3421 0.243095 GCAACCTACGTCGTTCCTCT 59.757 55.000 1.78 0.00 0.00 3.69
898 3687 0.879400 CGCTCCAGCTTAGCATCCAG 60.879 60.000 16.09 0.00 40.08 3.86
933 3786 0.252467 CTTCTCCCTCACCCCAGAGT 60.252 60.000 0.00 0.00 33.75 3.24
940 3811 3.717294 CACCCCAGAGTTCCCGGG 61.717 72.222 16.85 16.85 41.71 5.73
955 3826 2.282180 GGGAGGCGGCAACTTTCA 60.282 61.111 13.08 0.00 0.00 2.69
958 3829 1.508088 GAGGCGGCAACTTTCATGG 59.492 57.895 13.08 0.00 0.00 3.66
1078 3973 1.082300 GACGACGACGACTGCAAGA 60.082 57.895 15.32 0.00 42.66 3.02
1145 4040 1.996191 GATGTCGTTCAAGAGCCTGAC 59.004 52.381 0.00 0.00 0.00 3.51
1317 4212 2.733593 GCCGTCGACGACAAGCTT 60.734 61.111 37.65 0.00 43.02 3.74
1449 4376 1.735973 GCCGGCCAGATCAATTTCC 59.264 57.895 18.11 0.00 0.00 3.13
1462 4389 1.067354 CAATTTCCAAGCCTGGCTGAC 60.067 52.381 24.16 0.00 43.17 3.51
1463 4390 0.407139 ATTTCCAAGCCTGGCTGACT 59.593 50.000 24.16 3.20 43.17 3.41
1464 4391 0.185901 TTTCCAAGCCTGGCTGACTT 59.814 50.000 24.16 2.75 43.17 3.01
1634 4588 4.555262 CACCTCTTCAAGAGTGAGTTCTC 58.445 47.826 13.58 0.00 40.72 2.87
1642 4596 1.617850 AGAGTGAGTTCTCCACTGCTG 59.382 52.381 0.00 0.00 44.14 4.41
1644 4598 1.765314 AGTGAGTTCTCCACTGCTGTT 59.235 47.619 0.00 0.00 42.68 3.16
1645 4599 2.139118 GTGAGTTCTCCACTGCTGTTC 58.861 52.381 0.00 0.00 35.01 3.18
1727 4840 4.329801 GCCTTCCAAAAGAACAACACTTTG 59.670 41.667 0.00 0.00 37.59 2.77
1728 4841 4.329801 CCTTCCAAAAGAACAACACTTTGC 59.670 41.667 0.00 0.00 37.59 3.68
1784 4920 8.893563 TTGGATATTTTTGTACTCCTGGAATT 57.106 30.769 0.00 0.00 0.00 2.17
1785 4921 9.983024 TTGGATATTTTTGTACTCCTGGAATTA 57.017 29.630 0.00 0.00 0.00 1.40
1803 4959 7.224297 TGGAATTAGAGTGCTTGAAAGTTACT 58.776 34.615 2.97 2.97 0.00 2.24
1865 5021 7.810658 ACATCATATTCGCTTTTAGGCATAAG 58.189 34.615 0.00 0.00 0.00 1.73
1956 5112 3.845259 GCAGACCCGCCGGTGATA 61.845 66.667 18.79 0.00 44.88 2.15
2017 5177 0.763035 AAGCCACCCGTAACTTCAGT 59.237 50.000 0.00 0.00 0.00 3.41
2027 5187 3.997021 CCGTAACTTCAGTCTTTCTGCAT 59.003 43.478 0.00 0.00 43.32 3.96
2064 5227 8.485591 CAGCTTTGAAAATGTCTCTTTCATTTC 58.514 33.333 4.72 0.00 42.31 2.17
2071 5234 6.487689 AATGTCTCTTTCATTTCGGAACTC 57.512 37.500 0.00 0.00 32.50 3.01
2130 5294 6.428083 TTCACACCTCTTATACACTGGAAA 57.572 37.500 0.00 0.00 0.00 3.13
2144 5308 6.877611 ACACTGGAAATACTACAAAACTGG 57.122 37.500 0.00 0.00 0.00 4.00
2147 5311 5.705905 ACTGGAAATACTACAAAACTGGCTC 59.294 40.000 0.00 0.00 0.00 4.70
2267 5501 7.856145 AACTTGAGAAAGCTTATATGACCTG 57.144 36.000 0.00 0.00 0.00 4.00
2307 5542 1.602377 GCTCACAGTAACACCCACAAC 59.398 52.381 0.00 0.00 0.00 3.32
2319 5554 8.161425 AGTAACACCCACAACTTAGTAATTCAT 58.839 33.333 0.00 0.00 0.00 2.57
2323 5558 9.528489 ACACCCACAACTTAGTAATTCATAAAT 57.472 29.630 0.00 0.00 0.00 1.40
2326 5561 9.301153 CCCACAACTTAGTAATTCATAAATTGC 57.699 33.333 4.56 0.00 37.64 3.56
2389 5625 7.750229 TGGAGAAAATATTCACCAGATATGC 57.250 36.000 3.99 0.00 47.00 3.14
2409 5645 2.761559 CCATTGTACGTCACTTGGTGA 58.238 47.619 0.00 0.00 40.50 4.02
2534 5771 1.228124 ACAACACGTGTCATGGGGG 60.228 57.895 23.61 8.18 34.38 5.40
2569 5806 3.062763 GGCTCCAGAATACATCATGACG 58.937 50.000 0.00 0.00 0.00 4.35
2570 5807 3.062763 GCTCCAGAATACATCATGACGG 58.937 50.000 0.00 0.00 0.00 4.79
2576 5813 0.768221 ATACATCATGACGGGGGCCT 60.768 55.000 0.84 0.00 0.00 5.19
2712 5949 1.409427 GCTAGACCATACCTCAAGCGT 59.591 52.381 0.00 0.00 0.00 5.07
2814 6051 2.426522 GCATACAAGTGTCTCAGCCAA 58.573 47.619 0.00 0.00 0.00 4.52
2914 6151 0.755686 GGGCCCATTTGTGTTCACAA 59.244 50.000 19.95 13.36 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.588252 GCATTGCACGAATCCGCTAT 59.412 50.000 3.15 0.00 39.95 2.97
1 2 0.461870 AGCATTGCACGAATCCGCTA 60.462 50.000 11.91 0.00 39.95 4.26
2 3 1.308069 AAGCATTGCACGAATCCGCT 61.308 50.000 11.91 0.00 39.95 5.52
3 4 0.376852 TAAGCATTGCACGAATCCGC 59.623 50.000 11.91 0.00 39.95 5.54
4 5 2.351418 TCTTAAGCATTGCACGAATCCG 59.649 45.455 11.91 0.00 42.50 4.18
5 6 4.285292 CATCTTAAGCATTGCACGAATCC 58.715 43.478 11.91 0.00 0.00 3.01
6 7 4.201950 ACCATCTTAAGCATTGCACGAATC 60.202 41.667 11.91 0.00 0.00 2.52
7 8 3.696051 ACCATCTTAAGCATTGCACGAAT 59.304 39.130 11.91 0.00 0.00 3.34
8 9 3.081061 ACCATCTTAAGCATTGCACGAA 58.919 40.909 11.91 0.82 0.00 3.85
9 10 2.710377 ACCATCTTAAGCATTGCACGA 58.290 42.857 11.91 1.80 0.00 4.35
10 11 3.173599 CAACCATCTTAAGCATTGCACG 58.826 45.455 11.91 0.00 0.00 5.34
11 12 4.178545 ACAACCATCTTAAGCATTGCAC 57.821 40.909 11.91 0.00 0.00 4.57
12 13 4.870123 AACAACCATCTTAAGCATTGCA 57.130 36.364 11.91 0.00 0.00 4.08
13 14 7.010460 GGAATAAACAACCATCTTAAGCATTGC 59.990 37.037 0.00 0.00 0.00 3.56
14 15 7.492344 GGGAATAAACAACCATCTTAAGCATTG 59.508 37.037 0.00 2.44 0.00 2.82
15 16 7.555965 GGGAATAAACAACCATCTTAAGCATT 58.444 34.615 0.00 0.00 0.00 3.56
16 17 6.183360 CGGGAATAAACAACCATCTTAAGCAT 60.183 38.462 0.00 0.00 0.00 3.79
17 18 5.124776 CGGGAATAAACAACCATCTTAAGCA 59.875 40.000 0.00 0.00 0.00 3.91
18 19 5.355910 TCGGGAATAAACAACCATCTTAAGC 59.644 40.000 0.00 0.00 0.00 3.09
19 20 6.995511 TCGGGAATAAACAACCATCTTAAG 57.004 37.500 0.00 0.00 0.00 1.85
20 21 7.573469 CGTTTCGGGAATAAACAACCATCTTAA 60.573 37.037 0.00 0.00 36.78 1.85
21 22 6.128227 CGTTTCGGGAATAAACAACCATCTTA 60.128 38.462 0.00 0.00 36.78 2.10
22 23 5.335348 CGTTTCGGGAATAAACAACCATCTT 60.335 40.000 0.00 0.00 36.78 2.40
23 24 4.155280 CGTTTCGGGAATAAACAACCATCT 59.845 41.667 0.00 0.00 36.78 2.90
24 25 4.408694 CGTTTCGGGAATAAACAACCATC 58.591 43.478 0.00 0.00 36.78 3.51
25 26 3.366577 GCGTTTCGGGAATAAACAACCAT 60.367 43.478 0.00 0.00 36.78 3.55
26 27 2.030981 GCGTTTCGGGAATAAACAACCA 60.031 45.455 0.00 0.00 36.78 3.67
27 28 2.227149 AGCGTTTCGGGAATAAACAACC 59.773 45.455 0.00 0.00 36.78 3.77
28 29 3.547649 AGCGTTTCGGGAATAAACAAC 57.452 42.857 0.00 0.00 36.78 3.32
29 30 5.883503 AATAGCGTTTCGGGAATAAACAA 57.116 34.783 0.00 0.00 36.78 2.83
30 31 7.556733 AATAATAGCGTTTCGGGAATAAACA 57.443 32.000 0.00 0.00 36.78 2.83
31 32 8.845942 AAAATAATAGCGTTTCGGGAATAAAC 57.154 30.769 0.00 0.00 34.25 2.01
32 33 8.130469 GGAAAATAATAGCGTTTCGGGAATAAA 58.870 33.333 0.00 0.00 33.05 1.40
33 34 7.499895 AGGAAAATAATAGCGTTTCGGGAATAA 59.500 33.333 0.00 0.00 33.05 1.40
34 35 6.993902 AGGAAAATAATAGCGTTTCGGGAATA 59.006 34.615 0.00 0.00 33.05 1.75
35 36 5.826208 AGGAAAATAATAGCGTTTCGGGAAT 59.174 36.000 0.00 0.00 33.05 3.01
36 37 5.187687 AGGAAAATAATAGCGTTTCGGGAA 58.812 37.500 0.00 0.00 33.05 3.97
37 38 4.773013 AGGAAAATAATAGCGTTTCGGGA 58.227 39.130 0.00 0.00 33.05 5.14
38 39 5.494632 AAGGAAAATAATAGCGTTTCGGG 57.505 39.130 0.00 0.00 33.05 5.14
39 40 8.126700 ACAATAAGGAAAATAATAGCGTTTCGG 58.873 33.333 0.00 0.00 33.05 4.30
40 41 8.943925 CACAATAAGGAAAATAATAGCGTTTCG 58.056 33.333 0.00 0.00 33.05 3.46
41 42 9.783256 ACACAATAAGGAAAATAATAGCGTTTC 57.217 29.630 0.00 0.00 0.00 2.78
71 72 8.528295 CGACACAAAAATGAATTTCGTAACTTT 58.472 29.630 0.00 0.00 0.00 2.66
72 73 7.166804 CCGACACAAAAATGAATTTCGTAACTT 59.833 33.333 0.00 0.00 0.00 2.66
73 74 6.635239 CCGACACAAAAATGAATTTCGTAACT 59.365 34.615 0.00 0.00 0.00 2.24
74 75 6.415573 ACCGACACAAAAATGAATTTCGTAAC 59.584 34.615 0.00 0.00 0.00 2.50
75 76 6.496571 ACCGACACAAAAATGAATTTCGTAA 58.503 32.000 0.00 0.00 0.00 3.18
76 77 6.017770 AGACCGACACAAAAATGAATTTCGTA 60.018 34.615 0.00 0.00 0.00 3.43
77 78 4.927422 ACCGACACAAAAATGAATTTCGT 58.073 34.783 0.00 0.00 0.00 3.85
78 79 5.212194 AGACCGACACAAAAATGAATTTCG 58.788 37.500 0.00 0.00 0.00 3.46
79 80 7.136119 TGTAGACCGACACAAAAATGAATTTC 58.864 34.615 0.00 0.00 0.00 2.17
80 81 7.033530 TGTAGACCGACACAAAAATGAATTT 57.966 32.000 0.00 0.00 0.00 1.82
81 82 6.627395 TGTAGACCGACACAAAAATGAATT 57.373 33.333 0.00 0.00 0.00 2.17
112 113 9.182214 CAGCCTTTGCATAATTAGGATACATAT 57.818 33.333 0.32 0.00 41.13 1.78
113 114 7.611467 CCAGCCTTTGCATAATTAGGATACATA 59.389 37.037 0.32 0.00 41.13 2.29
114 115 6.435277 CCAGCCTTTGCATAATTAGGATACAT 59.565 38.462 0.32 0.00 41.13 2.29
115 116 5.769662 CCAGCCTTTGCATAATTAGGATACA 59.230 40.000 0.32 0.00 41.13 2.29
116 117 5.183904 CCCAGCCTTTGCATAATTAGGATAC 59.816 44.000 0.32 0.00 41.13 2.24
117 118 5.162991 ACCCAGCCTTTGCATAATTAGGATA 60.163 40.000 0.32 0.00 41.13 2.59
118 119 4.154942 CCCAGCCTTTGCATAATTAGGAT 58.845 43.478 0.32 0.00 41.13 3.24
119 120 3.052944 ACCCAGCCTTTGCATAATTAGGA 60.053 43.478 0.32 0.00 41.13 2.94
120 121 3.068590 CACCCAGCCTTTGCATAATTAGG 59.931 47.826 0.00 0.00 41.13 2.69
121 122 3.701040 ACACCCAGCCTTTGCATAATTAG 59.299 43.478 0.00 0.00 41.13 1.73
122 123 3.446873 CACACCCAGCCTTTGCATAATTA 59.553 43.478 0.00 0.00 41.13 1.40
123 124 2.234414 CACACCCAGCCTTTGCATAATT 59.766 45.455 0.00 0.00 41.13 1.40
124 125 1.826720 CACACCCAGCCTTTGCATAAT 59.173 47.619 0.00 0.00 41.13 1.28
125 126 1.202989 TCACACCCAGCCTTTGCATAA 60.203 47.619 0.00 0.00 41.13 1.90
126 127 0.403655 TCACACCCAGCCTTTGCATA 59.596 50.000 0.00 0.00 41.13 3.14
127 128 1.153524 TCACACCCAGCCTTTGCAT 59.846 52.632 0.00 0.00 41.13 3.96
128 129 1.827789 GTCACACCCAGCCTTTGCA 60.828 57.895 0.00 0.00 41.13 4.08
129 130 1.518903 GAGTCACACCCAGCCTTTGC 61.519 60.000 0.00 0.00 37.95 3.68
130 131 0.179020 TGAGTCACACCCAGCCTTTG 60.179 55.000 0.00 0.00 0.00 2.77
131 132 0.773644 ATGAGTCACACCCAGCCTTT 59.226 50.000 0.00 0.00 0.00 3.11
132 133 1.656587 TATGAGTCACACCCAGCCTT 58.343 50.000 0.00 0.00 0.00 4.35
133 134 1.656587 TTATGAGTCACACCCAGCCT 58.343 50.000 0.00 0.00 0.00 4.58
134 135 2.717639 ATTATGAGTCACACCCAGCC 57.282 50.000 0.00 0.00 0.00 4.85
135 136 6.699575 AAAATATTATGAGTCACACCCAGC 57.300 37.500 0.00 0.00 0.00 4.85
136 137 9.613428 TCTTAAAATATTATGAGTCACACCCAG 57.387 33.333 0.00 0.00 0.00 4.45
154 155 7.751793 CGCCGTTGGTTTTTACTATCTTAAAAT 59.248 33.333 0.00 0.00 32.33 1.82
155 156 7.076983 CGCCGTTGGTTTTTACTATCTTAAAA 58.923 34.615 0.00 0.00 0.00 1.52
156 157 6.348376 CCGCCGTTGGTTTTTACTATCTTAAA 60.348 38.462 0.00 0.00 0.00 1.52
157 158 5.122082 CCGCCGTTGGTTTTTACTATCTTAA 59.878 40.000 0.00 0.00 0.00 1.85
158 159 4.630940 CCGCCGTTGGTTTTTACTATCTTA 59.369 41.667 0.00 0.00 0.00 2.10
159 160 3.437741 CCGCCGTTGGTTTTTACTATCTT 59.562 43.478 0.00 0.00 0.00 2.40
160 161 3.004862 CCGCCGTTGGTTTTTACTATCT 58.995 45.455 0.00 0.00 0.00 1.98
161 162 3.002102 TCCGCCGTTGGTTTTTACTATC 58.998 45.455 0.00 0.00 0.00 2.08
162 163 3.004862 CTCCGCCGTTGGTTTTTACTAT 58.995 45.455 0.00 0.00 0.00 2.12
163 164 2.415776 CTCCGCCGTTGGTTTTTACTA 58.584 47.619 0.00 0.00 0.00 1.82
164 165 1.232119 CTCCGCCGTTGGTTTTTACT 58.768 50.000 0.00 0.00 0.00 2.24
165 166 0.386352 GCTCCGCCGTTGGTTTTTAC 60.386 55.000 0.00 0.00 0.00 2.01
166 167 0.535553 AGCTCCGCCGTTGGTTTTTA 60.536 50.000 0.00 0.00 0.00 1.52
167 168 1.388837 AAGCTCCGCCGTTGGTTTTT 61.389 50.000 0.00 0.00 0.00 1.94
168 169 0.535553 TAAGCTCCGCCGTTGGTTTT 60.536 50.000 0.00 0.00 0.00 2.43
169 170 0.953960 CTAAGCTCCGCCGTTGGTTT 60.954 55.000 0.00 0.00 0.00 3.27
170 171 1.375523 CTAAGCTCCGCCGTTGGTT 60.376 57.895 0.00 0.00 0.00 3.67
171 172 2.108278 AACTAAGCTCCGCCGTTGGT 62.108 55.000 0.00 0.00 0.00 3.67
172 173 1.375523 AACTAAGCTCCGCCGTTGG 60.376 57.895 0.00 0.00 0.00 3.77
173 174 0.669318 TCAACTAAGCTCCGCCGTTG 60.669 55.000 0.00 0.00 35.01 4.10
174 175 0.389948 CTCAACTAAGCTCCGCCGTT 60.390 55.000 0.00 0.00 0.00 4.44
175 176 1.215647 CTCAACTAAGCTCCGCCGT 59.784 57.895 0.00 0.00 0.00 5.68
176 177 1.519455 CCTCAACTAAGCTCCGCCG 60.519 63.158 0.00 0.00 0.00 6.46
177 178 1.815840 GCCTCAACTAAGCTCCGCC 60.816 63.158 0.00 0.00 0.00 6.13
178 179 1.815840 GGCCTCAACTAAGCTCCGC 60.816 63.158 0.00 0.00 0.00 5.54
179 180 0.460987 CAGGCCTCAACTAAGCTCCG 60.461 60.000 0.00 0.00 0.00 4.63
180 181 0.746204 GCAGGCCTCAACTAAGCTCC 60.746 60.000 0.00 0.00 0.00 4.70
181 182 0.036010 TGCAGGCCTCAACTAAGCTC 60.036 55.000 0.00 0.00 0.00 4.09
182 183 0.035630 CTGCAGGCCTCAACTAAGCT 60.036 55.000 0.00 0.00 0.00 3.74
183 184 1.028868 CCTGCAGGCCTCAACTAAGC 61.029 60.000 22.33 1.09 0.00 3.09
184 185 0.393537 CCCTGCAGGCCTCAACTAAG 60.394 60.000 28.39 5.53 0.00 2.18
185 186 1.685224 CCCTGCAGGCCTCAACTAA 59.315 57.895 28.39 0.00 0.00 2.24
186 187 2.300967 CCCCTGCAGGCCTCAACTA 61.301 63.158 28.39 0.00 0.00 2.24
187 188 3.655211 CCCCTGCAGGCCTCAACT 61.655 66.667 28.39 0.00 0.00 3.16
204 205 2.006805 TAAAGCTAGGGGGCCATGGC 62.007 60.000 29.47 29.47 41.06 4.40
205 206 0.178990 GTAAAGCTAGGGGGCCATGG 60.179 60.000 7.63 7.63 0.00 3.66
206 207 0.846693 AGTAAAGCTAGGGGGCCATG 59.153 55.000 4.39 0.00 0.00 3.66
207 208 2.055579 GTAGTAAAGCTAGGGGGCCAT 58.944 52.381 4.39 0.00 0.00 4.40
208 209 1.273953 TGTAGTAAAGCTAGGGGGCCA 60.274 52.381 4.39 0.00 0.00 5.36
209 210 1.503800 TGTAGTAAAGCTAGGGGGCC 58.496 55.000 0.00 0.00 0.00 5.80
210 211 3.639672 TTTGTAGTAAAGCTAGGGGGC 57.360 47.619 0.00 0.00 0.00 5.80
211 212 3.937079 CGTTTTGTAGTAAAGCTAGGGGG 59.063 47.826 0.00 0.00 0.00 5.40
212 213 3.937079 CCGTTTTGTAGTAAAGCTAGGGG 59.063 47.826 0.00 0.00 0.00 4.79
213 214 3.373130 GCCGTTTTGTAGTAAAGCTAGGG 59.627 47.826 0.00 0.00 0.00 3.53
214 215 3.998341 TGCCGTTTTGTAGTAAAGCTAGG 59.002 43.478 0.00 0.00 0.00 3.02
215 216 5.600908 TTGCCGTTTTGTAGTAAAGCTAG 57.399 39.130 0.00 0.00 0.00 3.42
216 217 5.470777 ACATTGCCGTTTTGTAGTAAAGCTA 59.529 36.000 0.00 0.00 0.00 3.32
217 218 4.277423 ACATTGCCGTTTTGTAGTAAAGCT 59.723 37.500 0.00 0.00 0.00 3.74
218 219 4.542735 ACATTGCCGTTTTGTAGTAAAGC 58.457 39.130 0.00 0.00 0.00 3.51
219 220 9.828852 TTAATACATTGCCGTTTTGTAGTAAAG 57.171 29.630 0.00 0.00 35.02 1.85
221 222 9.991388 GATTAATACATTGCCGTTTTGTAGTAA 57.009 29.630 5.15 5.15 39.33 2.24
222 223 8.614346 GGATTAATACATTGCCGTTTTGTAGTA 58.386 33.333 0.00 0.00 30.03 1.82
223 224 7.477494 GGATTAATACATTGCCGTTTTGTAGT 58.523 34.615 0.00 0.00 30.03 2.73
224 225 6.631238 CGGATTAATACATTGCCGTTTTGTAG 59.369 38.462 0.00 0.00 34.45 2.74
225 226 6.487960 CGGATTAATACATTGCCGTTTTGTA 58.512 36.000 0.00 0.00 34.45 2.41
226 227 5.336744 CGGATTAATACATTGCCGTTTTGT 58.663 37.500 0.00 0.00 34.45 2.83
227 228 5.864830 CGGATTAATACATTGCCGTTTTG 57.135 39.130 0.00 0.00 34.45 2.44
234 235 5.666969 TGCAGTACGGATTAATACATTGC 57.333 39.130 0.00 2.64 0.00 3.56
273 274 9.136952 TCGCTTACTTTCTTTACTGTCTATTTC 57.863 33.333 0.00 0.00 0.00 2.17
337 339 7.779754 AATTATTTGTTACCCCGTTTTACCT 57.220 32.000 0.00 0.00 0.00 3.08
380 382 2.539953 CGGTTGTTCTACAGCGCAAAAA 60.540 45.455 11.47 0.00 29.43 1.94
384 386 0.037697 ATCGGTTGTTCTACAGCGCA 60.038 50.000 11.47 0.00 33.92 6.09
385 387 0.370273 CATCGGTTGTTCTACAGCGC 59.630 55.000 0.00 0.00 33.92 5.92
386 388 1.990799 TCATCGGTTGTTCTACAGCG 58.009 50.000 0.00 0.00 29.43 5.18
461 1750 8.328758 AGGATGATTAAACTGACTATTCAACCA 58.671 33.333 0.00 0.00 30.16 3.67
462 1751 8.738645 AGGATGATTAAACTGACTATTCAACC 57.261 34.615 0.00 0.00 0.00 3.77
564 1872 1.837538 AATGTCACACCGCGGTTTCG 61.838 55.000 32.11 20.97 39.81 3.46
639 3358 2.315925 ACAGCCGATGATGTTCGATT 57.684 45.000 0.00 0.00 38.06 3.34
649 3368 4.749245 AAAGTAAGTGAAACAGCCGATG 57.251 40.909 0.00 0.00 41.43 3.84
651 3370 4.201970 CCAAAAAGTAAGTGAAACAGCCGA 60.202 41.667 0.00 0.00 41.43 5.54
653 3372 5.257082 TCCAAAAAGTAAGTGAAACAGCC 57.743 39.130 0.00 0.00 41.43 4.85
656 3375 5.511363 TCCCTCCAAAAAGTAAGTGAAACA 58.489 37.500 0.00 0.00 41.43 2.83
657 3376 5.009710 CCTCCCTCCAAAAAGTAAGTGAAAC 59.990 44.000 0.00 0.00 0.00 2.78
658 3377 5.137551 CCTCCCTCCAAAAAGTAAGTGAAA 58.862 41.667 0.00 0.00 0.00 2.69
659 3378 4.447180 CCCTCCCTCCAAAAAGTAAGTGAA 60.447 45.833 0.00 0.00 0.00 3.18
660 3379 3.073946 CCCTCCCTCCAAAAAGTAAGTGA 59.926 47.826 0.00 0.00 0.00 3.41
661 3380 3.421844 CCCTCCCTCCAAAAAGTAAGTG 58.578 50.000 0.00 0.00 0.00 3.16
662 3381 2.378886 CCCCTCCCTCCAAAAAGTAAGT 59.621 50.000 0.00 0.00 0.00 2.24
663 3382 2.884304 GCCCCTCCCTCCAAAAAGTAAG 60.884 54.545 0.00 0.00 0.00 2.34
664 3383 1.076513 GCCCCTCCCTCCAAAAAGTAA 59.923 52.381 0.00 0.00 0.00 2.24
665 3384 0.702316 GCCCCTCCCTCCAAAAAGTA 59.298 55.000 0.00 0.00 0.00 2.24
666 3385 1.368268 TGCCCCTCCCTCCAAAAAGT 61.368 55.000 0.00 0.00 0.00 2.66
667 3386 0.178935 TTGCCCCTCCCTCCAAAAAG 60.179 55.000 0.00 0.00 0.00 2.27
668 3387 0.471022 GTTGCCCCTCCCTCCAAAAA 60.471 55.000 0.00 0.00 0.00 1.94
669 3388 1.155155 GTTGCCCCTCCCTCCAAAA 59.845 57.895 0.00 0.00 0.00 2.44
670 3389 2.851045 GTTGCCCCTCCCTCCAAA 59.149 61.111 0.00 0.00 0.00 3.28
671 3390 2.424989 TAGGTTGCCCCTCCCTCCAA 62.425 60.000 0.00 0.00 44.81 3.53
672 3391 2.887846 TAGGTTGCCCCTCCCTCCA 61.888 63.158 0.00 0.00 44.81 3.86
673 3392 2.042261 TAGGTTGCCCCTCCCTCC 59.958 66.667 0.00 0.00 44.81 4.30
674 3393 2.732619 CGTAGGTTGCCCCTCCCTC 61.733 68.421 0.00 0.00 44.81 4.30
675 3394 2.687566 CGTAGGTTGCCCCTCCCT 60.688 66.667 0.00 0.00 44.81 4.20
676 3395 3.007323 ACGTAGGTTGCCCCTCCC 61.007 66.667 0.00 0.00 44.81 4.30
677 3396 2.582978 GACGTAGGTTGCCCCTCC 59.417 66.667 0.00 0.00 44.81 4.30
678 3397 2.163601 AACGACGTAGGTTGCCCCTC 62.164 60.000 0.00 0.00 44.81 4.30
680 3399 1.739196 GAACGACGTAGGTTGCCCC 60.739 63.158 0.00 0.00 0.00 5.80
681 3400 1.739196 GGAACGACGTAGGTTGCCC 60.739 63.158 0.00 2.39 30.54 5.36
682 3401 0.735287 GAGGAACGACGTAGGTTGCC 60.735 60.000 16.36 12.89 36.51 4.52
683 3402 0.243095 AGAGGAACGACGTAGGTTGC 59.757 55.000 13.37 13.37 36.16 4.17
684 3403 1.268899 ACAGAGGAACGACGTAGGTTG 59.731 52.381 0.00 1.13 0.00 3.77
694 3413 2.202492 CGGCGAGACAGAGGAACG 60.202 66.667 0.00 0.00 0.00 3.95
695 3414 1.310933 TACCGGCGAGACAGAGGAAC 61.311 60.000 9.30 0.00 0.00 3.62
696 3415 1.001764 TACCGGCGAGACAGAGGAA 60.002 57.895 9.30 0.00 0.00 3.36
699 3418 0.809385 TTTCTACCGGCGAGACAGAG 59.191 55.000 9.30 0.00 0.00 3.35
702 3421 1.210931 CGTTTCTACCGGCGAGACA 59.789 57.895 9.30 0.00 0.00 3.41
817 3580 3.499737 CACGGATGGGCTCGTTGC 61.500 66.667 0.00 0.00 37.53 4.17
888 3675 1.451927 CGGCTTGGCTGGATGCTAA 60.452 57.895 0.00 0.00 42.39 3.09
898 3687 3.909086 AAGGTGAGCTCGGCTTGGC 62.909 63.158 9.64 0.00 39.88 4.52
940 3811 1.244019 ACCATGAAAGTTGCCGCCTC 61.244 55.000 0.00 0.00 0.00 4.70
943 3814 1.212751 GGACCATGAAAGTTGCCGC 59.787 57.895 0.00 0.00 0.00 6.53
944 3815 1.200020 GAAGGACCATGAAAGTTGCCG 59.800 52.381 0.00 0.00 0.00 5.69
947 3818 6.316140 TCAATATCGAAGGACCATGAAAGTTG 59.684 38.462 0.00 0.00 0.00 3.16
955 3826 8.134202 TGTATATGTCAATATCGAAGGACCAT 57.866 34.615 0.00 0.00 31.27 3.55
1340 4235 1.870055 GAGGTACTTGACGGCGACCA 61.870 60.000 16.62 8.43 41.55 4.02
1449 4376 6.311445 CGTATAATATAAGTCAGCCAGGCTTG 59.689 42.308 12.86 7.94 43.35 4.01
1463 4390 9.985730 CCTACAAGAACAACCCGTATAATATAA 57.014 33.333 0.00 0.00 0.00 0.98
1464 4391 8.090214 GCCTACAAGAACAACCCGTATAATATA 58.910 37.037 0.00 0.00 0.00 0.86
1634 4588 2.291741 GGACAAAGAAGAACAGCAGTGG 59.708 50.000 0.00 0.00 0.00 4.00
1642 4596 3.821748 ACTTGAGGGGACAAAGAAGAAC 58.178 45.455 0.00 0.00 32.38 3.01
1644 4598 4.166144 AGAAACTTGAGGGGACAAAGAAGA 59.834 41.667 0.00 0.00 32.38 2.87
1645 4599 4.464947 AGAAACTTGAGGGGACAAAGAAG 58.535 43.478 0.00 0.00 32.38 2.85
1774 4910 4.478206 TCAAGCACTCTAATTCCAGGAG 57.522 45.455 0.00 0.00 0.00 3.69
1776 4912 5.006386 ACTTTCAAGCACTCTAATTCCAGG 58.994 41.667 0.00 0.00 0.00 4.45
1777 4913 6.566197 AACTTTCAAGCACTCTAATTCCAG 57.434 37.500 0.00 0.00 0.00 3.86
1778 4914 7.224297 AGTAACTTTCAAGCACTCTAATTCCA 58.776 34.615 0.00 0.00 0.00 3.53
1780 4916 9.425577 AGTAGTAACTTTCAAGCACTCTAATTC 57.574 33.333 0.00 0.00 29.00 2.17
1784 4920 7.762588 AGAGTAGTAACTTTCAAGCACTCTA 57.237 36.000 0.00 0.00 39.64 2.43
1785 4921 6.658188 AGAGTAGTAACTTTCAAGCACTCT 57.342 37.500 0.00 0.00 37.32 3.24
1803 4959 1.162698 CTCCACGTCGACCAAGAGTA 58.837 55.000 10.58 0.00 0.00 2.59
1865 5021 2.060980 ATCCACGGGAGAGAGCCAC 61.061 63.158 0.00 0.00 34.05 5.01
1956 5112 1.207329 GAGGCCTTGAAGTCACGGTAT 59.793 52.381 6.77 0.00 37.56 2.73
2027 5187 7.491682 ACATTTTCAAAGCTGCTTCTTTTCTA 58.508 30.769 16.28 0.00 34.31 2.10
2064 5227 2.824341 AGTAACCACCACTAGAGTTCCG 59.176 50.000 0.00 0.00 0.00 4.30
2071 5234 5.646360 CCCATTTGTTAGTAACCACCACTAG 59.354 44.000 10.51 0.00 30.48 2.57
2130 5294 4.455877 GCTTGTGAGCCAGTTTTGTAGTAT 59.544 41.667 0.00 0.00 43.29 2.12
2164 5328 7.989741 AGGTTCAAAATCTAGATTCGACATCAT 59.010 33.333 18.19 6.76 0.00 2.45
2203 5367 3.010027 TGGCATCTTGGATGGTTCAACTA 59.990 43.478 9.18 0.00 0.00 2.24
2267 5501 3.445096 AGCTTGATTTATGTGGTGAAGCC 59.555 43.478 0.00 0.00 35.93 4.35
2307 5542 9.571810 TTGCACTGCAATTTATGAATTACTAAG 57.428 29.630 12.59 0.00 43.99 2.18
2355 5590 9.057089 GGTGAATATTTTCTCCAACTAGGTATG 57.943 37.037 10.89 0.00 42.53 2.39
2375 5610 4.756642 CGTACAATGGCATATCTGGTGAAT 59.243 41.667 0.00 0.00 0.00 2.57
2382 5618 4.672587 AGTGACGTACAATGGCATATCT 57.327 40.909 0.00 0.00 0.00 1.98
2383 5619 4.024893 CCAAGTGACGTACAATGGCATATC 60.025 45.833 0.00 0.00 33.23 1.63
2389 5625 2.761559 TCACCAAGTGACGTACAATGG 58.238 47.619 14.15 14.15 37.67 3.16
2409 5645 8.771286 AGCATTGGAATTTTGTAAGGGAAATAT 58.229 29.630 0.00 0.00 0.00 1.28
2712 5949 6.427853 CCATGACTTTGTACAATCTGTCAGAA 59.572 38.462 27.42 15.34 37.76 3.02
2814 6051 1.154430 TGGGCCTAGACTTTGGGTTT 58.846 50.000 4.53 0.00 0.00 3.27
2914 6151 2.240667 CCTTGTCCTCCTCCACAATGAT 59.759 50.000 0.00 0.00 32.13 2.45


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

AutoCloner maintained by Alex Coulton.