Multiple sequence alignment - TraesCS7B01G137200

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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 TraesCS7B01G137200 chr7B 100.000 5003 0 0 1 5003 169432034 169437036 0.000000e+00 9239.0
1 TraesCS7B01G137200 chr7B 88.095 840 69 20 1344 2153 32330805 32331643 0.000000e+00 968.0
2 TraesCS7B01G137200 chr7B 92.980 641 45 0 1344 1984 32344796 32345436 0.000000e+00 935.0
3 TraesCS7B01G137200 chr7B 92.756 635 46 0 1344 1978 32408645 32409279 0.000000e+00 918.0
4 TraesCS7B01G137200 chr7B 89.981 529 36 11 4475 5003 743283491 743284002 0.000000e+00 667.0
5 TraesCS7B01G137200 chr7B 85.657 502 47 15 2268 2745 32331754 32332254 5.780000e-139 505.0
6 TraesCS7B01G137200 chr7B 93.722 223 14 0 1018 1240 32330516 32330738 8.030000e-88 335.0
7 TraesCS7B01G137200 chr7B 87.143 280 32 3 999 1277 650130060 650129784 1.050000e-81 315.0
8 TraesCS7B01G137200 chr7B 89.200 250 27 0 2268 2517 32409540 32409789 3.760000e-81 313.0
9 TraesCS7B01G137200 chr7B 81.481 216 27 7 2771 2980 32410561 32410769 1.110000e-36 165.0
10 TraesCS7B01G137200 chr7B 89.024 82 8 1 2582 2663 32348291 32348371 3.190000e-17 100.0
11 TraesCS7B01G137200 chr7A 93.790 3462 139 25 715 4129 217202371 217205803 0.000000e+00 5132.0
12 TraesCS7B01G137200 chr7A 89.186 823 72 13 1344 2162 84854955 84855764 0.000000e+00 1011.0
13 TraesCS7B01G137200 chr7A 84.867 978 115 24 1018 1988 674275164 674274213 0.000000e+00 955.0
14 TraesCS7B01G137200 chr7A 92.587 634 47 0 1344 1977 85031192 85031825 0.000000e+00 911.0
15 TraesCS7B01G137200 chr7A 83.144 706 90 16 2268 2963 84855868 84856554 7.120000e-173 617.0
16 TraesCS7B01G137200 chr7A 95.720 257 9 1 4168 4422 217205802 217206058 3.600000e-111 412.0
17 TraesCS7B01G137200 chr7A 85.596 361 40 8 2609 2960 674273774 674273417 7.910000e-98 368.0
18 TraesCS7B01G137200 chr7A 93.274 223 15 0 1018 1240 84854670 84854892 3.730000e-86 329.0
19 TraesCS7B01G137200 chr7A 89.328 253 27 0 2268 2520 85032127 85032379 8.080000e-83 318.0
20 TraesCS7B01G137200 chr7A 90.323 217 21 0 1018 1234 85030873 85031089 8.200000e-73 285.0
21 TraesCS7B01G137200 chr7A 89.796 98 10 0 3920 4017 85033203 85033300 5.260000e-25 126.0
22 TraesCS7B01G137200 chr7A 94.286 35 0 2 4424 4456 217206079 217206113 9.000000e-03 52.8
23 TraesCS7B01G137200 chr7D 93.653 2978 127 31 662 3610 205131399 205134343 0.000000e+00 4396.0
24 TraesCS7B01G137200 chr7D 82.855 1464 155 51 1344 2745 83063539 83064968 0.000000e+00 1225.0
25 TraesCS7B01G137200 chr7D 84.990 986 124 20 1000 1983 582304002 582303039 0.000000e+00 979.0
26 TraesCS7B01G137200 chr7D 93.189 646 42 2 1344 1988 82899315 82899959 0.000000e+00 948.0
27 TraesCS7B01G137200 chr7D 90.803 598 39 14 3542 4129 205134235 205134826 0.000000e+00 785.0
28 TraesCS7B01G137200 chr7D 82.277 931 117 29 2041 2961 82901808 82902700 0.000000e+00 761.0
29 TraesCS7B01G137200 chr7D 91.698 530 36 8 4475 5003 472800477 472799955 0.000000e+00 728.0
30 TraesCS7B01G137200 chr7D 89.189 592 32 16 79 664 205130547 205131112 0.000000e+00 710.0
31 TraesCS7B01G137200 chr7D 94.141 256 9 3 4168 4422 205134825 205135075 7.860000e-103 385.0
32 TraesCS7B01G137200 chr7D 93.722 223 14 0 1018 1240 82899030 82899252 8.030000e-88 335.0
33 TraesCS7B01G137200 chr7D 91.244 217 19 0 1018 1234 83063229 83063445 3.790000e-76 296.0
34 TraesCS7B01G137200 chr7D 76.307 287 54 14 1351 1630 263506276 263505997 1.880000e-29 141.0
35 TraesCS7B01G137200 chr7D 97.500 40 1 0 4417 4456 205135088 205135127 8.990000e-08 69.4
36 TraesCS7B01G137200 chr7D 97.222 36 1 0 2108 2143 35560283 35560318 1.500000e-05 62.1
37 TraesCS7B01G137200 chr5D 92.817 529 31 5 4475 5003 23177321 23176800 0.000000e+00 760.0
38 TraesCS7B01G137200 chr5D 92.105 532 28 6 4472 5003 219763645 219764162 0.000000e+00 737.0
39 TraesCS7B01G137200 chr5B 92.439 529 25 4 4475 5003 93460345 93460858 0.000000e+00 741.0
40 TraesCS7B01G137200 chr4D 92.322 521 22 2 4483 5003 85172180 85171678 0.000000e+00 725.0
41 TraesCS7B01G137200 chr4D 74.064 374 85 12 1343 1710 44422854 44423221 5.220000e-30 143.0
42 TraesCS7B01G137200 chr4D 79.762 168 24 6 1344 1506 470232347 470232509 4.090000e-21 113.0
43 TraesCS7B01G137200 chr3D 91.825 526 23 6 4478 5003 433536585 433536080 0.000000e+00 715.0
44 TraesCS7B01G137200 chr6D 91.445 526 26 7 4478 5003 309989252 309988746 0.000000e+00 704.0
45 TraesCS7B01G137200 chr6D 75.868 576 107 26 1344 1903 462690095 462690654 1.070000e-66 265.0
46 TraesCS7B01G137200 chr6D 73.594 640 123 36 1349 1962 462635750 462635131 2.360000e-48 204.0
47 TraesCS7B01G137200 chr6D 93.182 132 8 1 4473 4604 309960446 309960316 5.110000e-45 193.0
48 TraesCS7B01G137200 chr2D 90.602 532 26 7 4475 5003 159336018 159335508 0.000000e+00 684.0
49 TraesCS7B01G137200 chrUn 90.840 524 27 7 4472 4995 95737217 95737719 0.000000e+00 682.0
50 TraesCS7B01G137200 chr4B 90.802 511 34 10 4496 5003 8383929 8384429 0.000000e+00 671.0
51 TraesCS7B01G137200 chr4B 81.098 164 29 2 1344 1506 592626983 592627145 4.060000e-26 130.0
52 TraesCS7B01G137200 chr2B 81.884 828 118 21 2274 3076 792123431 792122611 0.000000e+00 669.0
53 TraesCS7B01G137200 chr2A 90.200 500 39 8 4504 5003 751179182 751179671 1.170000e-180 643.0
54 TraesCS7B01G137200 chr6A 76.256 577 103 26 1344 1903 609551875 609552434 4.930000e-70 276.0
55 TraesCS7B01G137200 chr6A 89.189 74 8 0 2087 2160 498580088 498580161 5.330000e-15 93.5
56 TraesCS7B01G137200 chr5A 79.670 182 35 2 1344 1524 552374831 552375011 4.060000e-26 130.0
57 TraesCS7B01G137200 chr4A 80.488 164 30 2 1344 1506 678128881 678129043 1.890000e-24 124.0


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 TraesCS7B01G137200 chr7B 169432034 169437036 5002 False 9239.000000 9239 100.000000 1 5003 1 chr7B.!!$F1 5002
1 TraesCS7B01G137200 chr7B 743283491 743284002 511 False 667.000000 667 89.981000 4475 5003 1 chr7B.!!$F2 528
2 TraesCS7B01G137200 chr7B 32330516 32332254 1738 False 602.666667 968 89.158000 1018 2745 3 chr7B.!!$F3 1727
3 TraesCS7B01G137200 chr7B 32344796 32348371 3575 False 517.500000 935 91.002000 1344 2663 2 chr7B.!!$F4 1319
4 TraesCS7B01G137200 chr7B 32408645 32410769 2124 False 465.333333 918 87.812333 1344 2980 3 chr7B.!!$F5 1636
5 TraesCS7B01G137200 chr7A 217202371 217206113 3742 False 1865.600000 5132 94.598667 715 4456 3 chr7A.!!$F3 3741
6 TraesCS7B01G137200 chr7A 674273417 674275164 1747 True 661.500000 955 85.231500 1018 2960 2 chr7A.!!$R1 1942
7 TraesCS7B01G137200 chr7A 84854670 84856554 1884 False 652.333333 1011 88.534667 1018 2963 3 chr7A.!!$F1 1945
8 TraesCS7B01G137200 chr7A 85030873 85033300 2427 False 410.000000 911 90.508500 1018 4017 4 chr7A.!!$F2 2999
9 TraesCS7B01G137200 chr7D 205130547 205135127 4580 False 1269.080000 4396 93.057200 79 4456 5 chr7D.!!$F4 4377
10 TraesCS7B01G137200 chr7D 582303039 582304002 963 True 979.000000 979 84.990000 1000 1983 1 chr7D.!!$R3 983
11 TraesCS7B01G137200 chr7D 83063229 83064968 1739 False 760.500000 1225 87.049500 1018 2745 2 chr7D.!!$F3 1727
12 TraesCS7B01G137200 chr7D 472799955 472800477 522 True 728.000000 728 91.698000 4475 5003 1 chr7D.!!$R2 528
13 TraesCS7B01G137200 chr7D 82899030 82902700 3670 False 681.333333 948 89.729333 1018 2961 3 chr7D.!!$F2 1943
14 TraesCS7B01G137200 chr5D 23176800 23177321 521 True 760.000000 760 92.817000 4475 5003 1 chr5D.!!$R1 528
15 TraesCS7B01G137200 chr5D 219763645 219764162 517 False 737.000000 737 92.105000 4472 5003 1 chr5D.!!$F1 531
16 TraesCS7B01G137200 chr5B 93460345 93460858 513 False 741.000000 741 92.439000 4475 5003 1 chr5B.!!$F1 528
17 TraesCS7B01G137200 chr4D 85171678 85172180 502 True 725.000000 725 92.322000 4483 5003 1 chr4D.!!$R1 520
18 TraesCS7B01G137200 chr3D 433536080 433536585 505 True 715.000000 715 91.825000 4478 5003 1 chr3D.!!$R1 525
19 TraesCS7B01G137200 chr6D 309988746 309989252 506 True 704.000000 704 91.445000 4478 5003 1 chr6D.!!$R2 525
20 TraesCS7B01G137200 chr6D 462690095 462690654 559 False 265.000000 265 75.868000 1344 1903 1 chr6D.!!$F1 559
21 TraesCS7B01G137200 chr6D 462635131 462635750 619 True 204.000000 204 73.594000 1349 1962 1 chr6D.!!$R3 613
22 TraesCS7B01G137200 chr2D 159335508 159336018 510 True 684.000000 684 90.602000 4475 5003 1 chr2D.!!$R1 528
23 TraesCS7B01G137200 chrUn 95737217 95737719 502 False 682.000000 682 90.840000 4472 4995 1 chrUn.!!$F1 523
24 TraesCS7B01G137200 chr4B 8383929 8384429 500 False 671.000000 671 90.802000 4496 5003 1 chr4B.!!$F1 507
25 TraesCS7B01G137200 chr2B 792122611 792123431 820 True 669.000000 669 81.884000 2274 3076 1 chr2B.!!$R1 802
26 TraesCS7B01G137200 chr6A 609551875 609552434 559 False 276.000000 276 76.256000 1344 1903 1 chr6A.!!$F2 559

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 0.108756 GGCACCCTGAACTAGTCGAC 60.109 60.000 7.70 7.7 0.0 4.20 F
339 345 0.756903 ACGCACACAGGGAGTTTAGT 59.243 50.000 0.00 0.0 0.0 2.24 F
1249 1557 0.533491 ATTCCTGGTACGTGCGCTAA 59.467 50.000 9.73 0.0 0.0 3.09 F
1572 1923 2.435693 GCTCTACATCCTGCCCGGT 61.436 63.158 0.00 0.0 0.0 5.28 F
2967 7531 1.834188 TCCTTCGCCCTTCCAAATTC 58.166 50.000 0.00 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1557 2.037620 GAGGAGATGGATGCTGGCGT 62.038 60.000 0.00 0.0 0.00 5.68 R
1333 1668 2.158971 TGCCGAGCTGCAACATATTAGA 60.159 45.455 1.02 0.0 38.56 2.10 R
2418 5954 0.381089 GCTCCACGTCGCTAGTGTAT 59.619 55.000 2.66 0.0 37.88 2.29 R
3320 7917 1.001406 CTTCTATGGATGGCCTCGGTC 59.999 57.143 3.32 0.0 34.31 4.79 R
4457 9102 0.537371 CAATAGGCCCGTTCCCATCC 60.537 60.000 0.00 0.0 0.00 3.51 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
25 26 3.894947 GCGCGAGGAGGAGAGGTC 61.895 72.222 12.10 0.00 0.00 3.85
26 27 3.213402 CGCGAGGAGGAGAGGTCC 61.213 72.222 0.00 0.00 44.33 4.46
34 35 3.787394 GGAGAGGTCCGGTCACAA 58.213 61.111 0.00 0.00 31.37 3.33
35 36 1.592223 GGAGAGGTCCGGTCACAAG 59.408 63.158 0.00 0.00 31.37 3.16
36 37 0.898789 GGAGAGGTCCGGTCACAAGA 60.899 60.000 0.00 0.00 31.37 3.02
37 38 0.528470 GAGAGGTCCGGTCACAAGAG 59.472 60.000 0.00 0.00 0.00 2.85
38 39 1.079750 GAGGTCCGGTCACAAGAGC 60.080 63.158 0.00 0.00 38.87 4.09
39 40 1.534235 AGGTCCGGTCACAAGAGCT 60.534 57.895 0.00 0.00 40.07 4.09
40 41 1.079750 GGTCCGGTCACAAGAGCTC 60.080 63.158 5.27 5.27 40.07 4.09
41 42 1.079750 GTCCGGTCACAAGAGCTCC 60.080 63.158 10.93 0.00 40.07 4.70
42 43 2.125912 CCGGTCACAAGAGCTCCG 60.126 66.667 10.93 5.34 40.07 4.63
43 44 2.811317 CGGTCACAAGAGCTCCGC 60.811 66.667 10.93 0.00 40.07 5.54
44 45 2.435059 GGTCACAAGAGCTCCGCC 60.435 66.667 10.93 0.08 39.16 6.13
45 46 2.435059 GTCACAAGAGCTCCGCCC 60.435 66.667 10.93 0.00 0.00 6.13
46 47 2.604686 TCACAAGAGCTCCGCCCT 60.605 61.111 10.93 0.00 0.00 5.19
47 48 1.304962 TCACAAGAGCTCCGCCCTA 60.305 57.895 10.93 0.00 0.00 3.53
48 49 1.153549 CACAAGAGCTCCGCCCTAC 60.154 63.158 10.93 0.00 0.00 3.18
49 50 2.359967 ACAAGAGCTCCGCCCTACC 61.360 63.158 10.93 0.00 0.00 3.18
50 51 2.764547 AAGAGCTCCGCCCTACCC 60.765 66.667 10.93 0.00 0.00 3.69
51 52 4.862823 AGAGCTCCGCCCTACCCC 62.863 72.222 10.93 0.00 0.00 4.95
53 54 4.733725 AGCTCCGCCCTACCCCAA 62.734 66.667 0.00 0.00 0.00 4.12
54 55 4.176752 GCTCCGCCCTACCCCAAG 62.177 72.222 0.00 0.00 0.00 3.61
55 56 3.480133 CTCCGCCCTACCCCAAGG 61.480 72.222 0.00 0.00 40.04 3.61
56 57 3.995809 CTCCGCCCTACCCCAAGGA 62.996 68.421 0.00 0.00 39.15 3.36
57 58 3.793888 CCGCCCTACCCCAAGGAC 61.794 72.222 0.00 0.00 39.15 3.85
58 59 3.006728 CGCCCTACCCCAAGGACA 61.007 66.667 0.00 0.00 39.15 4.02
59 60 2.998949 GCCCTACCCCAAGGACAG 59.001 66.667 0.00 0.00 39.15 3.51
60 61 1.615424 GCCCTACCCCAAGGACAGA 60.615 63.158 0.00 0.00 39.15 3.41
61 62 1.205460 GCCCTACCCCAAGGACAGAA 61.205 60.000 0.00 0.00 39.15 3.02
62 63 0.912486 CCCTACCCCAAGGACAGAAG 59.088 60.000 0.00 0.00 39.15 2.85
63 64 1.657804 CCTACCCCAAGGACAGAAGT 58.342 55.000 0.00 0.00 39.15 3.01
64 65 2.561297 CCCTACCCCAAGGACAGAAGTA 60.561 54.545 0.00 0.00 39.15 2.24
65 66 3.178865 CCTACCCCAAGGACAGAAGTAA 58.821 50.000 0.00 0.00 39.15 2.24
66 67 3.585732 CCTACCCCAAGGACAGAAGTAAA 59.414 47.826 0.00 0.00 39.15 2.01
67 68 3.790089 ACCCCAAGGACAGAAGTAAAG 57.210 47.619 0.00 0.00 36.73 1.85
68 69 3.053826 ACCCCAAGGACAGAAGTAAAGT 58.946 45.455 0.00 0.00 36.73 2.66
69 70 3.072622 ACCCCAAGGACAGAAGTAAAGTC 59.927 47.826 0.00 0.00 36.73 3.01
74 75 2.593257 GGACAGAAGTAAAGTCCGTCG 58.407 52.381 0.00 0.00 42.02 5.12
75 76 2.593257 GACAGAAGTAAAGTCCGTCGG 58.407 52.381 4.39 4.39 0.00 4.79
76 77 1.959282 ACAGAAGTAAAGTCCGTCGGT 59.041 47.619 11.88 0.00 0.00 4.69
77 78 2.030451 ACAGAAGTAAAGTCCGTCGGTC 60.030 50.000 11.88 5.68 0.00 4.79
78 79 2.228343 CAGAAGTAAAGTCCGTCGGTCT 59.772 50.000 11.88 8.37 0.00 3.85
79 80 2.889678 AGAAGTAAAGTCCGTCGGTCTT 59.110 45.455 16.66 16.66 32.89 3.01
80 81 3.320256 AGAAGTAAAGTCCGTCGGTCTTT 59.680 43.478 30.16 30.16 42.01 2.52
81 82 4.520492 AGAAGTAAAGTCCGTCGGTCTTTA 59.480 41.667 28.50 28.50 40.39 1.85
82 83 4.431661 AGTAAAGTCCGTCGGTCTTTAG 57.568 45.455 31.09 0.65 41.32 1.85
83 84 2.075979 AAAGTCCGTCGGTCTTTAGC 57.924 50.000 27.76 5.95 38.76 3.09
164 165 7.239763 TGTGGGTTTTTCTCTTCTTTCTTTT 57.760 32.000 0.00 0.00 0.00 2.27
165 166 7.096551 TGTGGGTTTTTCTCTTCTTTCTTTTG 58.903 34.615 0.00 0.00 0.00 2.44
166 167 7.097192 GTGGGTTTTTCTCTTCTTTCTTTTGT 58.903 34.615 0.00 0.00 0.00 2.83
167 168 7.063426 GTGGGTTTTTCTCTTCTTTCTTTTGTG 59.937 37.037 0.00 0.00 0.00 3.33
168 169 7.097192 GGGTTTTTCTCTTCTTTCTTTTGTGT 58.903 34.615 0.00 0.00 0.00 3.72
169 170 7.275779 GGGTTTTTCTCTTCTTTCTTTTGTGTC 59.724 37.037 0.00 0.00 0.00 3.67
170 171 8.029522 GGTTTTTCTCTTCTTTCTTTTGTGTCT 58.970 33.333 0.00 0.00 0.00 3.41
171 172 9.411801 GTTTTTCTCTTCTTTCTTTTGTGTCTT 57.588 29.630 0.00 0.00 0.00 3.01
174 175 8.786826 TTCTCTTCTTTCTTTTGTGTCTTACA 57.213 30.769 0.00 0.00 37.56 2.41
175 176 8.964476 TCTCTTCTTTCTTTTGTGTCTTACAT 57.036 30.769 0.00 0.00 39.48 2.29
176 177 9.396022 TCTCTTCTTTCTTTTGTGTCTTACATT 57.604 29.630 0.00 0.00 39.48 2.71
196 197 3.695830 TTAGTTGGCACCCTGAACTAG 57.304 47.619 0.00 0.00 34.51 2.57
201 202 0.108756 GGCACCCTGAACTAGTCGAC 60.109 60.000 7.70 7.70 0.00 4.20
205 206 3.672781 GCACCCTGAACTAGTCGACTTAC 60.673 52.174 25.44 12.83 0.00 2.34
207 208 4.217983 CACCCTGAACTAGTCGACTTACTT 59.782 45.833 25.44 12.27 0.00 2.24
209 210 5.303845 ACCCTGAACTAGTCGACTTACTTTT 59.696 40.000 25.44 9.71 0.00 2.27
244 246 8.575649 AAATAGTACTCCCATTTAGTTGGTTG 57.424 34.615 0.00 0.00 34.77 3.77
255 257 7.338196 CCCATTTAGTTGGTTGTGTGTATCATA 59.662 37.037 0.00 0.00 34.77 2.15
272 274 4.521130 TCATAATGATGTAGAGGCCGAC 57.479 45.455 0.00 0.00 34.41 4.79
289 291 3.005367 GCCGACTTCTCCCATTTTCAAAA 59.995 43.478 0.00 0.00 0.00 2.44
322 328 6.201044 CACACATAGAGGCTAAATTCCTAACG 59.799 42.308 0.00 0.00 33.24 3.18
339 345 0.756903 ACGCACACAGGGAGTTTAGT 59.243 50.000 0.00 0.00 0.00 2.24
343 349 3.412386 GCACACAGGGAGTTTAGTTGAT 58.588 45.455 0.00 0.00 0.00 2.57
344 350 4.575885 GCACACAGGGAGTTTAGTTGATA 58.424 43.478 0.00 0.00 0.00 2.15
401 407 5.852282 AATCATACAAGTTATGGTTGCCC 57.148 39.130 0.00 0.00 28.06 5.36
403 409 2.116827 TACAAGTTATGGTTGCCCCG 57.883 50.000 0.00 0.00 35.15 5.73
418 424 1.596603 CCCCGTTCCGTGTTAAAACT 58.403 50.000 0.00 0.00 0.00 2.66
420 426 2.358582 CCCCGTTCCGTGTTAAAACTTT 59.641 45.455 0.00 0.00 0.00 2.66
421 427 3.548616 CCCCGTTCCGTGTTAAAACTTTC 60.549 47.826 0.00 0.00 0.00 2.62
429 436 8.648968 GTTCCGTGTTAAAACTTTCAAAAATGA 58.351 29.630 0.00 0.00 0.00 2.57
449 456 6.566079 ATGATGGTTCATGAGAGTTAGGAA 57.434 37.500 0.00 0.00 41.12 3.36
460 467 4.039730 TGAGAGTTAGGAAGCATATGAGGC 59.960 45.833 6.97 0.00 0.00 4.70
521 528 2.097304 TGAATCATTGCCAATTCGGACG 59.903 45.455 0.00 0.00 36.56 4.79
566 573 4.135306 TCTCTCGGGTCTATGACATGTAC 58.865 47.826 0.00 0.00 33.68 2.90
567 574 3.883489 CTCTCGGGTCTATGACATGTACA 59.117 47.826 0.00 0.00 33.68 2.90
640 647 5.108385 TCTTTCTTTTGCGGAGAACATTC 57.892 39.130 0.00 0.00 33.15 2.67
676 972 2.675348 GTGACTTATGAGTGAGCTTGCC 59.325 50.000 0.00 0.00 35.88 4.52
684 980 1.523938 GTGAGCTTGCCGGTATCCC 60.524 63.158 1.90 0.00 0.00 3.85
689 985 1.133262 AGCTTGCCGGTATCCCTACTA 60.133 52.381 1.90 0.00 0.00 1.82
699 995 3.453353 GGTATCCCTACTACTGGTTTGCA 59.547 47.826 0.00 0.00 0.00 4.08
712 1008 4.019174 CTGGTTTGCATAGGGATGAACTT 58.981 43.478 0.00 0.00 34.73 2.66
713 1009 5.186256 TGGTTTGCATAGGGATGAACTTA 57.814 39.130 0.00 0.00 34.73 2.24
740 1036 2.638855 TGCCATTTCCTCCTGCAAAAAT 59.361 40.909 0.00 0.00 0.00 1.82
743 1039 5.221803 TGCCATTTCCTCCTGCAAAAATAAA 60.222 36.000 0.00 0.00 0.00 1.40
787 1083 3.118738 AGTCCCGTGGATTCATAACTGAC 60.119 47.826 0.00 0.00 32.73 3.51
788 1084 2.835156 TCCCGTGGATTCATAACTGACA 59.165 45.455 0.00 0.00 0.00 3.58
789 1085 3.454447 TCCCGTGGATTCATAACTGACAT 59.546 43.478 0.00 0.00 0.00 3.06
794 1090 4.747108 GTGGATTCATAACTGACATCGAGG 59.253 45.833 0.00 0.00 0.00 4.63
796 1092 5.596772 TGGATTCATAACTGACATCGAGGTA 59.403 40.000 1.11 0.00 0.00 3.08
820 1116 3.432252 CCTAATCTCACGGACACAAACAC 59.568 47.826 0.00 0.00 0.00 3.32
873 1170 2.772515 GCTACCTACCCAGTGGATCTTT 59.227 50.000 11.95 0.00 34.81 2.52
882 1179 2.761208 CCAGTGGATCTTTACTCCTCGT 59.239 50.000 1.68 0.00 33.69 4.18
886 1183 4.712337 AGTGGATCTTTACTCCTCGTTCAT 59.288 41.667 0.00 0.00 33.69 2.57
889 1186 5.302059 TGGATCTTTACTCCTCGTTCATAGG 59.698 44.000 0.00 0.00 33.69 2.57
967 1264 4.344865 GAGCCGCAGACCCCCAAA 62.345 66.667 0.00 0.00 0.00 3.28
968 1265 4.660938 AGCCGCAGACCCCCAAAC 62.661 66.667 0.00 0.00 0.00 2.93
973 1270 2.265904 GCAGACCCCCAAACCGAAC 61.266 63.158 0.00 0.00 0.00 3.95
995 1292 4.548513 CCGAGGGAGGGAGGAGGG 62.549 77.778 0.00 0.00 0.00 4.30
996 1293 4.548513 CGAGGGAGGGAGGAGGGG 62.549 77.778 0.00 0.00 0.00 4.79
997 1294 4.179599 GAGGGAGGGAGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
1249 1557 0.533491 ATTCCTGGTACGTGCGCTAA 59.467 50.000 9.73 0.00 0.00 3.09
1274 1583 2.967201 CAGCATCCATCTCCTCTTCTCT 59.033 50.000 0.00 0.00 0.00 3.10
1278 1587 3.311167 TCCATCTCCTCTTCTCTCCAG 57.689 52.381 0.00 0.00 0.00 3.86
1285 1594 2.507992 CTTCTCTCCAGCACGGCG 60.508 66.667 4.80 4.80 33.14 6.46
1326 1661 4.383173 CATACCATTGCTGTCTGCTGATA 58.617 43.478 3.20 0.00 43.37 2.15
1327 1662 2.915349 ACCATTGCTGTCTGCTGATAG 58.085 47.619 12.19 12.19 43.37 2.08
1329 1664 3.452264 ACCATTGCTGTCTGCTGATAGTA 59.548 43.478 16.66 10.89 43.37 1.82
1331 1666 5.061853 CCATTGCTGTCTGCTGATAGTAAT 58.938 41.667 21.13 21.13 43.38 1.89
1332 1667 6.183361 ACCATTGCTGTCTGCTGATAGTAATA 60.183 38.462 24.29 7.53 41.78 0.98
1333 1668 6.877855 CCATTGCTGTCTGCTGATAGTAATAT 59.122 38.462 24.29 9.72 41.78 1.28
1334 1669 7.064371 CCATTGCTGTCTGCTGATAGTAATATC 59.936 40.741 24.29 3.21 41.78 1.63
1335 1670 6.907853 TGCTGTCTGCTGATAGTAATATCT 57.092 37.500 16.66 0.00 43.37 1.98
1572 1923 2.435693 GCTCTACATCCTGCCCGGT 61.436 63.158 0.00 0.00 0.00 5.28
2038 3116 7.545965 TCAACTCTCTTTCGAATATTCTGAACC 59.454 37.037 13.45 0.00 0.00 3.62
2178 5614 9.474920 CAGGCTAATTCAAATTTCAAAACTGTA 57.525 29.630 0.00 0.00 0.00 2.74
2179 5615 9.696917 AGGCTAATTCAAATTTCAAAACTGTAG 57.303 29.630 0.00 0.00 0.00 2.74
2412 5948 5.582689 TGATCTTCAGAGATAACTTCGCA 57.417 39.130 0.00 0.00 42.66 5.10
2418 5954 5.262588 TCAGAGATAACTTCGCAAGCATA 57.737 39.130 0.00 0.00 37.18 3.14
2720 7168 2.832129 TCTCCTCGGCTACAAGTTCAAT 59.168 45.455 0.00 0.00 0.00 2.57
2967 7531 1.834188 TCCTTCGCCCTTCCAAATTC 58.166 50.000 0.00 0.00 0.00 2.17
3024 7612 5.705609 TTAAAAAGTCAACTGGAGGATGC 57.294 39.130 0.00 0.00 0.00 3.91
3253 7850 4.570369 CGGTTGATGCACACAGTCATATAA 59.430 41.667 0.00 0.00 0.00 0.98
3583 8187 5.182487 TGGAGTATGCACATAATTGTCGTT 58.818 37.500 0.00 0.00 32.34 3.85
3629 8233 0.892755 ATCAACCGTTCTACCGCTGA 59.107 50.000 0.00 0.00 0.00 4.26
3641 8245 1.067084 CCGCTGATGATGACTCGCT 59.933 57.895 0.00 0.00 0.00 4.93
3644 8248 1.001924 CGCTGATGATGACTCGCTAGT 60.002 52.381 0.00 0.00 39.21 2.57
3688 8298 0.548989 AAATACCACCCATGCCGCTA 59.451 50.000 0.00 0.00 0.00 4.26
3713 8323 1.207791 AACATCGGGAGCAGGAAGAT 58.792 50.000 0.00 0.00 0.00 2.40
3755 8365 1.227527 CACTGTCACACCGCCTTCA 60.228 57.895 0.00 0.00 0.00 3.02
3948 8569 4.229479 GCGCTAGCTTCAAGCCGC 62.229 66.667 14.43 14.43 43.77 6.53
4044 8665 8.604890 GTTTATCTCCCTCTTTATTCTTTGACG 58.395 37.037 0.00 0.00 0.00 4.35
4045 8666 4.504858 TCTCCCTCTTTATTCTTTGACGC 58.495 43.478 0.00 0.00 0.00 5.19
4099 8720 6.051717 ACCATGGAAATTCTTCGAGTATCAG 58.948 40.000 21.47 0.00 33.17 2.90
4127 8748 5.949952 GGTATGGAAACCAGGTTGAATAACT 59.050 40.000 5.30 0.00 39.50 2.24
4128 8749 7.114095 GGTATGGAAACCAGGTTGAATAACTA 58.886 38.462 5.30 0.00 39.50 2.24
4129 8750 7.066645 GGTATGGAAACCAGGTTGAATAACTAC 59.933 40.741 5.30 2.45 39.50 2.73
4130 8751 6.195600 TGGAAACCAGGTTGAATAACTACT 57.804 37.500 5.30 0.00 36.99 2.57
4131 8752 6.235664 TGGAAACCAGGTTGAATAACTACTC 58.764 40.000 5.30 0.00 36.99 2.59
4132 8753 6.183361 TGGAAACCAGGTTGAATAACTACTCA 60.183 38.462 5.30 0.00 36.99 3.41
4133 8754 6.884836 GGAAACCAGGTTGAATAACTACTCAT 59.115 38.462 5.30 0.00 36.99 2.90
4134 8755 7.393515 GGAAACCAGGTTGAATAACTACTCATT 59.606 37.037 5.30 0.00 36.99 2.57
4135 8756 8.706322 AAACCAGGTTGAATAACTACTCATTT 57.294 30.769 5.30 0.00 36.99 2.32
4136 8757 8.706322 AACCAGGTTGAATAACTACTCATTTT 57.294 30.769 3.18 0.00 36.99 1.82
4137 8758 8.706322 ACCAGGTTGAATAACTACTCATTTTT 57.294 30.769 0.00 0.00 36.99 1.94
4158 8779 5.705609 TTTTGAGCCTGAATAGTGGAAAC 57.294 39.130 0.00 0.00 0.00 2.78
4159 8780 3.350219 TGAGCCTGAATAGTGGAAACC 57.650 47.619 0.00 0.00 0.00 3.27
4160 8781 2.642311 TGAGCCTGAATAGTGGAAACCA 59.358 45.455 0.00 0.00 0.00 3.67
4161 8782 3.266772 TGAGCCTGAATAGTGGAAACCAT 59.733 43.478 0.00 0.00 35.28 3.55
4162 8783 4.473196 TGAGCCTGAATAGTGGAAACCATA 59.527 41.667 0.00 0.00 35.28 2.74
4163 8784 5.041191 AGCCTGAATAGTGGAAACCATAG 57.959 43.478 0.00 0.00 35.28 2.23
4164 8785 4.137543 GCCTGAATAGTGGAAACCATAGG 58.862 47.826 0.00 0.00 35.28 2.57
4165 8786 4.141482 GCCTGAATAGTGGAAACCATAGGA 60.141 45.833 0.00 0.00 35.28 2.94
4166 8787 5.615289 CCTGAATAGTGGAAACCATAGGAG 58.385 45.833 0.00 0.00 35.28 3.69
4204 8827 4.675565 CGTTATGAGCCTGAATAGTGTACG 59.324 45.833 0.00 0.00 0.00 3.67
4395 9018 8.647796 AGACTTTTTAGGGTATTTCTTTTTGGG 58.352 33.333 0.00 0.00 0.00 4.12
4456 9101 8.742125 ACTATAGGATTGAGAAATATGGGTCA 57.258 34.615 4.43 0.00 0.00 4.02
4457 9102 8.820831 ACTATAGGATTGAGAAATATGGGTCAG 58.179 37.037 4.43 0.00 0.00 3.51
4458 9103 5.316158 AGGATTGAGAAATATGGGTCAGG 57.684 43.478 0.00 0.00 0.00 3.86
4459 9104 4.977739 AGGATTGAGAAATATGGGTCAGGA 59.022 41.667 0.00 0.00 0.00 3.86
4460 9105 5.614402 AGGATTGAGAAATATGGGTCAGGAT 59.386 40.000 0.00 0.00 0.00 3.24
4461 9106 5.709164 GGATTGAGAAATATGGGTCAGGATG 59.291 44.000 0.00 0.00 37.54 3.51
4462 9107 4.712051 TGAGAAATATGGGTCAGGATGG 57.288 45.455 0.00 0.00 36.16 3.51
4463 9108 3.395607 TGAGAAATATGGGTCAGGATGGG 59.604 47.826 0.00 0.00 36.16 4.00
4464 9109 3.652869 GAGAAATATGGGTCAGGATGGGA 59.347 47.826 0.00 0.00 36.16 4.37
4465 9110 4.054369 AGAAATATGGGTCAGGATGGGAA 58.946 43.478 0.00 0.00 36.16 3.97
4466 9111 3.884037 AATATGGGTCAGGATGGGAAC 57.116 47.619 0.00 0.00 36.16 3.62
4467 9112 1.128200 TATGGGTCAGGATGGGAACG 58.872 55.000 0.00 0.00 36.16 3.95
4468 9113 1.635817 ATGGGTCAGGATGGGAACGG 61.636 60.000 0.00 0.00 36.16 4.44
4469 9114 2.590092 GGTCAGGATGGGAACGGG 59.410 66.667 0.00 0.00 36.16 5.28
4470 9115 2.124695 GTCAGGATGGGAACGGGC 60.125 66.667 0.00 0.00 36.16 6.13
4471 9116 3.407967 TCAGGATGGGAACGGGCC 61.408 66.667 0.00 0.00 36.16 5.80
4472 9117 3.411517 CAGGATGGGAACGGGCCT 61.412 66.667 0.84 0.00 0.00 5.19
4473 9118 2.070039 CAGGATGGGAACGGGCCTA 61.070 63.158 0.84 0.00 0.00 3.93
4490 9135 5.163457 CGGGCCTATTGGATAAAACAACAAT 60.163 40.000 0.84 0.00 37.34 2.71
4607 9254 3.867857 ACACATCTAACACACACACACA 58.132 40.909 0.00 0.00 0.00 3.72
4608 9255 3.621268 ACACATCTAACACACACACACAC 59.379 43.478 0.00 0.00 0.00 3.82
4609 9256 3.620821 CACATCTAACACACACACACACA 59.379 43.478 0.00 0.00 0.00 3.72
4610 9257 3.621268 ACATCTAACACACACACACACAC 59.379 43.478 0.00 0.00 0.00 3.82
4611 9258 2.623535 TCTAACACACACACACACACC 58.376 47.619 0.00 0.00 0.00 4.16
4612 9259 1.668751 CTAACACACACACACACACCC 59.331 52.381 0.00 0.00 0.00 4.61
4613 9260 0.037590 AACACACACACACACACCCT 59.962 50.000 0.00 0.00 0.00 4.34
4652 9313 3.289407 TGGTGGATCAACAACACTGAA 57.711 42.857 1.86 0.00 32.08 3.02
4694 9355 2.202544 CGCTCGAGTCTGTGCCTC 60.203 66.667 15.13 0.00 0.00 4.70
4755 9416 2.682856 GTGAAGAGCGAGAGTCTGATCT 59.317 50.000 0.00 0.73 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.894947 GACCTCTCCTCCTCGCGC 61.895 72.222 0.00 0.00 0.00 6.86
9 10 3.213402 GGACCTCTCCTCCTCGCG 61.213 72.222 0.00 0.00 33.07 5.87
10 11 3.213402 CGGACCTCTCCTCCTCGC 61.213 72.222 0.00 0.00 33.79 5.03
11 12 2.517402 CCGGACCTCTCCTCCTCG 60.517 72.222 0.00 0.00 33.79 4.63
12 13 1.454295 GACCGGACCTCTCCTCCTC 60.454 68.421 9.46 0.00 33.79 3.71
13 14 2.239439 TGACCGGACCTCTCCTCCT 61.239 63.158 9.46 0.00 33.79 3.69
14 15 2.053277 GTGACCGGACCTCTCCTCC 61.053 68.421 9.46 0.00 33.79 4.30
15 16 0.898789 TTGTGACCGGACCTCTCCTC 60.899 60.000 9.46 0.00 33.79 3.71
16 17 0.900647 CTTGTGACCGGACCTCTCCT 60.901 60.000 9.46 0.00 33.79 3.69
17 18 0.898789 TCTTGTGACCGGACCTCTCC 60.899 60.000 9.46 0.00 0.00 3.71
18 19 0.528470 CTCTTGTGACCGGACCTCTC 59.472 60.000 9.46 0.00 0.00 3.20
19 20 1.536943 GCTCTTGTGACCGGACCTCT 61.537 60.000 9.46 0.00 0.00 3.69
20 21 1.079750 GCTCTTGTGACCGGACCTC 60.080 63.158 9.46 0.00 0.00 3.85
21 22 1.534235 AGCTCTTGTGACCGGACCT 60.534 57.895 9.46 0.00 0.00 3.85
22 23 1.079750 GAGCTCTTGTGACCGGACC 60.080 63.158 9.46 0.00 0.00 4.46
23 24 1.079750 GGAGCTCTTGTGACCGGAC 60.080 63.158 9.46 1.07 0.00 4.79
24 25 2.636412 CGGAGCTCTTGTGACCGGA 61.636 63.158 9.46 0.00 39.92 5.14
25 26 2.125912 CGGAGCTCTTGTGACCGG 60.126 66.667 14.64 0.00 39.92 5.28
38 39 3.480133 CCTTGGGGTAGGGCGGAG 61.480 72.222 0.00 0.00 0.00 4.63
39 40 4.014075 TCCTTGGGGTAGGGCGGA 62.014 66.667 0.00 0.00 35.90 5.54
40 41 3.793888 GTCCTTGGGGTAGGGCGG 61.794 72.222 0.00 0.00 35.90 6.13
41 42 3.006728 TGTCCTTGGGGTAGGGCG 61.007 66.667 0.00 0.00 43.04 6.13
42 43 1.205460 TTCTGTCCTTGGGGTAGGGC 61.205 60.000 0.00 0.00 40.44 5.19
43 44 0.912486 CTTCTGTCCTTGGGGTAGGG 59.088 60.000 0.00 0.00 35.90 3.53
44 45 1.657804 ACTTCTGTCCTTGGGGTAGG 58.342 55.000 0.00 0.00 36.59 3.18
45 46 4.286291 ACTTTACTTCTGTCCTTGGGGTAG 59.714 45.833 0.00 0.00 0.00 3.18
46 47 4.237018 ACTTTACTTCTGTCCTTGGGGTA 58.763 43.478 0.00 0.00 0.00 3.69
47 48 3.053826 ACTTTACTTCTGTCCTTGGGGT 58.946 45.455 0.00 0.00 0.00 4.95
48 49 3.559384 GGACTTTACTTCTGTCCTTGGGG 60.559 52.174 0.00 0.00 44.84 4.96
49 50 3.676093 GGACTTTACTTCTGTCCTTGGG 58.324 50.000 0.00 0.00 44.84 4.12
50 51 3.244112 ACGGACTTTACTTCTGTCCTTGG 60.244 47.826 9.30 0.00 45.75 3.61
51 52 3.988517 GACGGACTTTACTTCTGTCCTTG 59.011 47.826 9.30 0.00 45.75 3.61
52 53 3.305199 CGACGGACTTTACTTCTGTCCTT 60.305 47.826 9.30 0.48 45.75 3.36
53 54 2.228343 CGACGGACTTTACTTCTGTCCT 59.772 50.000 9.30 0.00 45.75 3.85
54 55 2.593257 CGACGGACTTTACTTCTGTCC 58.407 52.381 5.87 0.00 43.74 4.02
55 56 2.030451 ACCGACGGACTTTACTTCTGTC 60.030 50.000 23.38 1.84 43.36 3.51
56 57 1.959282 ACCGACGGACTTTACTTCTGT 59.041 47.619 23.38 0.00 35.17 3.41
57 58 2.228343 AGACCGACGGACTTTACTTCTG 59.772 50.000 23.38 0.00 0.00 3.02
58 59 2.512705 AGACCGACGGACTTTACTTCT 58.487 47.619 23.38 7.26 0.00 2.85
59 60 3.294816 AAGACCGACGGACTTTACTTC 57.705 47.619 23.08 7.22 34.38 3.01
60 61 3.740631 AAAGACCGACGGACTTTACTT 57.259 42.857 32.95 16.41 43.41 2.24
61 62 3.366781 GCTAAAGACCGACGGACTTTACT 60.367 47.826 33.07 21.08 43.41 2.24
62 63 2.919859 GCTAAAGACCGACGGACTTTAC 59.080 50.000 33.07 26.87 43.41 2.01
63 64 2.821969 AGCTAAAGACCGACGGACTTTA 59.178 45.455 33.68 33.68 43.41 1.85
64 65 1.617357 AGCTAAAGACCGACGGACTTT 59.383 47.619 34.74 34.74 45.93 2.66
65 66 1.067776 CAGCTAAAGACCGACGGACTT 60.068 52.381 23.08 23.08 39.14 3.01
66 67 0.526662 CAGCTAAAGACCGACGGACT 59.473 55.000 23.38 17.98 0.00 3.85
67 68 0.524862 TCAGCTAAAGACCGACGGAC 59.475 55.000 23.38 15.55 0.00 4.79
68 69 0.524862 GTCAGCTAAAGACCGACGGA 59.475 55.000 23.38 0.00 0.00 4.69
69 70 0.242825 TGTCAGCTAAAGACCGACGG 59.757 55.000 13.61 13.61 35.15 4.79
70 71 1.920574 CATGTCAGCTAAAGACCGACG 59.079 52.381 0.62 0.00 35.15 5.12
71 72 2.924290 GACATGTCAGCTAAAGACCGAC 59.076 50.000 21.07 0.00 35.15 4.79
72 73 2.560981 TGACATGTCAGCTAAAGACCGA 59.439 45.455 24.56 0.00 35.15 4.69
73 74 2.959516 TGACATGTCAGCTAAAGACCG 58.040 47.619 24.56 0.00 35.15 4.79
74 75 6.985188 TTAATGACATGTCAGCTAAAGACC 57.015 37.500 30.63 0.30 43.61 3.85
75 76 9.534565 TCTATTAATGACATGTCAGCTAAAGAC 57.465 33.333 30.63 0.83 43.61 3.01
126 127 4.946478 AACCCACAATCAATCGGAAAAA 57.054 36.364 0.00 0.00 0.00 1.94
133 134 6.986250 AGAAGAGAAAAACCCACAATCAATC 58.014 36.000 0.00 0.00 0.00 2.67
164 165 4.517453 GGTGCCAACTAAATGTAAGACACA 59.483 41.667 0.00 0.00 42.69 3.72
165 166 4.082949 GGGTGCCAACTAAATGTAAGACAC 60.083 45.833 0.00 0.00 0.00 3.67
166 167 4.076394 GGGTGCCAACTAAATGTAAGACA 58.924 43.478 0.00 0.00 0.00 3.41
167 168 4.156008 CAGGGTGCCAACTAAATGTAAGAC 59.844 45.833 0.00 0.00 0.00 3.01
168 169 4.042311 TCAGGGTGCCAACTAAATGTAAGA 59.958 41.667 0.00 0.00 0.00 2.10
169 170 4.331968 TCAGGGTGCCAACTAAATGTAAG 58.668 43.478 0.00 0.00 0.00 2.34
170 171 4.374689 TCAGGGTGCCAACTAAATGTAA 57.625 40.909 0.00 0.00 0.00 2.41
171 172 4.076394 GTTCAGGGTGCCAACTAAATGTA 58.924 43.478 0.00 0.00 0.00 2.29
172 173 2.890945 GTTCAGGGTGCCAACTAAATGT 59.109 45.455 0.00 0.00 0.00 2.71
173 174 3.157087 AGTTCAGGGTGCCAACTAAATG 58.843 45.455 0.00 0.00 0.00 2.32
174 175 3.525800 AGTTCAGGGTGCCAACTAAAT 57.474 42.857 0.00 0.00 0.00 1.40
175 176 3.393278 ACTAGTTCAGGGTGCCAACTAAA 59.607 43.478 0.00 0.00 33.30 1.85
176 177 2.976882 ACTAGTTCAGGGTGCCAACTAA 59.023 45.455 0.00 0.00 33.30 2.24
177 178 2.565834 GACTAGTTCAGGGTGCCAACTA 59.434 50.000 0.00 0.00 32.56 2.24
223 225 5.163131 ACACAACCAACTAAATGGGAGTACT 60.163 40.000 0.00 0.00 45.18 2.73
224 226 5.048991 CACACAACCAACTAAATGGGAGTAC 60.049 44.000 0.00 0.00 45.18 2.73
225 227 5.067273 CACACAACCAACTAAATGGGAGTA 58.933 41.667 0.00 0.00 45.18 2.59
226 228 3.888930 CACACAACCAACTAAATGGGAGT 59.111 43.478 0.00 0.00 45.18 3.85
227 229 3.888930 ACACACAACCAACTAAATGGGAG 59.111 43.478 0.00 0.00 45.18 4.30
228 230 3.904717 ACACACAACCAACTAAATGGGA 58.095 40.909 0.00 0.00 45.18 4.37
229 231 5.475220 TGATACACACAACCAACTAAATGGG 59.525 40.000 0.00 0.00 45.18 4.00
230 232 6.567687 TGATACACACAACCAACTAAATGG 57.432 37.500 0.00 0.00 46.38 3.16
233 235 9.508642 TCATTATGATACACACAACCAACTAAA 57.491 29.630 0.00 0.00 0.00 1.85
234 236 9.679661 ATCATTATGATACACACAACCAACTAA 57.320 29.630 5.83 0.00 34.88 2.24
235 237 9.108284 CATCATTATGATACACACAACCAACTA 57.892 33.333 7.44 0.00 34.28 2.24
244 246 6.591834 GGCCTCTACATCATTATGATACACAC 59.408 42.308 7.44 0.00 34.28 3.82
255 257 3.034635 AGAAGTCGGCCTCTACATCATT 58.965 45.455 0.00 0.00 0.00 2.57
272 274 6.035975 GTGTGTGTTTTTGAAAATGGGAGAAG 59.964 38.462 0.00 0.00 0.00 2.85
289 291 2.104792 AGCCTCTATGTGTGTGTGTGTT 59.895 45.455 0.00 0.00 0.00 3.32
322 328 2.846193 TCAACTAAACTCCCTGTGTGC 58.154 47.619 0.00 0.00 0.00 4.57
403 409 8.648968 TCATTTTTGAAAGTTTTAACACGGAAC 58.351 29.630 0.00 0.00 0.00 3.62
418 424 7.954835 ACTCTCATGAACCATCATTTTTGAAA 58.045 30.769 0.00 0.00 43.89 2.69
420 426 7.528996 AACTCTCATGAACCATCATTTTTGA 57.471 32.000 0.00 0.00 43.89 2.69
421 427 7.972277 CCTAACTCTCATGAACCATCATTTTTG 59.028 37.037 0.00 0.00 43.89 2.44
429 436 4.225942 TGCTTCCTAACTCTCATGAACCAT 59.774 41.667 0.00 0.00 0.00 3.55
438 445 4.565022 GCCTCATATGCTTCCTAACTCTC 58.435 47.826 0.00 0.00 0.00 3.20
460 467 0.947244 GGCATATCTTGGGAAGCACG 59.053 55.000 0.00 0.00 0.00 5.34
566 573 0.673437 AAAATGTGAGGCAACCGGTG 59.327 50.000 8.52 3.35 37.17 4.94
567 574 1.408969 AAAAATGTGAGGCAACCGGT 58.591 45.000 0.00 0.00 37.17 5.28
603 610 9.377383 GCAAAAGAAAGAATGAAAATGACAATG 57.623 29.630 0.00 0.00 0.00 2.82
607 614 6.420604 TCCGCAAAAGAAAGAATGAAAATGAC 59.579 34.615 0.00 0.00 0.00 3.06
619 626 3.908382 CGAATGTTCTCCGCAAAAGAAAG 59.092 43.478 0.00 0.00 34.68 2.62
640 647 9.425893 CTCATAAGTCACTGTAATTAAATTGCG 57.574 33.333 0.00 0.00 0.00 4.85
684 980 5.070446 TCATCCCTATGCAAACCAGTAGTAG 59.930 44.000 0.00 0.00 32.76 2.57
689 985 3.010584 AGTTCATCCCTATGCAAACCAGT 59.989 43.478 0.00 0.00 32.76 4.00
712 1008 6.138391 TGCAGGAGGAAATGGCATATTATA 57.862 37.500 0.00 0.00 0.00 0.98
713 1009 5.001833 TGCAGGAGGAAATGGCATATTAT 57.998 39.130 0.00 0.00 0.00 1.28
743 1039 2.368548 GGCCCCACAATGTCTTCTTTTT 59.631 45.455 0.00 0.00 0.00 1.94
787 1083 3.365465 CGTGAGATTAGGCTACCTCGATG 60.365 52.174 14.63 8.38 34.61 3.84
788 1084 2.814919 CGTGAGATTAGGCTACCTCGAT 59.185 50.000 14.63 0.00 34.61 3.59
789 1085 2.219458 CGTGAGATTAGGCTACCTCGA 58.781 52.381 14.63 0.00 34.61 4.04
794 1090 2.426024 TGTGTCCGTGAGATTAGGCTAC 59.574 50.000 0.00 0.00 0.00 3.58
796 1092 1.557099 TGTGTCCGTGAGATTAGGCT 58.443 50.000 0.00 0.00 0.00 4.58
873 1170 4.981812 TCTATGCCTATGAACGAGGAGTA 58.018 43.478 0.00 0.00 35.99 2.59
886 1183 1.960471 GCCCTCGGCTATCTATGCCTA 60.960 57.143 3.23 0.00 46.69 3.93
889 1186 4.921834 GCCCTCGGCTATCTATGC 57.078 61.111 0.00 0.00 46.69 3.14
955 1252 2.114411 TTCGGTTTGGGGGTCTGC 59.886 61.111 0.00 0.00 0.00 4.26
1249 1557 2.037620 GAGGAGATGGATGCTGGCGT 62.038 60.000 0.00 0.00 0.00 5.68
1285 1594 2.436646 ACTATGCAGTGCGGTGCC 60.437 61.111 11.20 0.00 43.28 5.01
1326 1661 7.761704 CCGAGCTGCAACATATTAGATATTACT 59.238 37.037 1.02 0.00 0.00 2.24
1327 1662 7.464710 GCCGAGCTGCAACATATTAGATATTAC 60.465 40.741 1.02 0.00 0.00 1.89
1329 1664 5.352569 GCCGAGCTGCAACATATTAGATATT 59.647 40.000 1.02 0.00 0.00 1.28
1331 1666 4.245660 GCCGAGCTGCAACATATTAGATA 58.754 43.478 1.02 0.00 0.00 1.98
1332 1667 3.070018 GCCGAGCTGCAACATATTAGAT 58.930 45.455 1.02 0.00 0.00 1.98
1333 1668 2.158971 TGCCGAGCTGCAACATATTAGA 60.159 45.455 1.02 0.00 38.56 2.10
1334 1669 2.212652 TGCCGAGCTGCAACATATTAG 58.787 47.619 1.02 0.00 38.56 1.73
1335 1670 2.323968 TGCCGAGCTGCAACATATTA 57.676 45.000 1.02 0.00 38.56 0.98
1572 1923 3.296709 GACGGCGAAGGAGAAGGCA 62.297 63.158 16.62 0.00 0.00 4.75
2178 5614 6.894339 AACAAGAATCACCGGTTTAATTCT 57.106 33.333 22.26 22.26 39.52 2.40
2179 5615 7.865889 AGAAAACAAGAATCACCGGTTTAATTC 59.134 33.333 19.49 19.49 31.94 2.17
2182 5618 6.702716 AGAAAACAAGAATCACCGGTTTAA 57.297 33.333 2.97 0.00 31.94 1.52
2412 5948 3.550233 CCACGTCGCTAGTGTATATGCTT 60.550 47.826 2.66 0.00 37.88 3.91
2418 5954 0.381089 GCTCCACGTCGCTAGTGTAT 59.619 55.000 2.66 0.00 37.88 2.29
2720 7168 8.285891 ACATAATCAATTACCCCAACTCCATAA 58.714 33.333 0.00 0.00 0.00 1.90
2790 7338 9.822185 ATGTCGCAGAATCATAGCATAAATATA 57.178 29.630 0.00 0.00 39.69 0.86
2967 7531 6.482641 TCATCACAAAATGAAAAACATGGTGG 59.517 34.615 0.00 0.00 41.93 4.61
3050 7640 9.420118 TGAGTTATTAAATTGGTGCCTATGAAT 57.580 29.630 0.00 0.00 0.00 2.57
3127 7718 6.183361 GCCCTCTGTTCCTATATCCAAAGTTA 60.183 42.308 0.00 0.00 0.00 2.24
3207 7803 1.852157 AGATGCCAGGGTTGGTCCA 60.852 57.895 0.00 0.00 46.80 4.02
3253 7850 9.573166 TGCTAGGCATTGTTGAATAACTAATAT 57.427 29.630 0.00 0.00 33.90 1.28
3320 7917 1.001406 CTTCTATGGATGGCCTCGGTC 59.999 57.143 3.32 0.00 34.31 4.79
3353 7951 3.139397 TGTAGGTTTGGGGAGATGTTGTT 59.861 43.478 0.00 0.00 0.00 2.83
3509 8110 4.142249 CGCATACTCCGGGTCATCATATTA 60.142 45.833 0.00 0.00 0.00 0.98
3532 8136 5.328886 TCATCATTCGACGACAATTATGC 57.671 39.130 0.00 0.00 0.00 3.14
3583 8187 8.833493 GTCAATTATGTGAGTCATCATCATTCA 58.167 33.333 10.30 0.00 37.87 2.57
3629 8233 3.006323 GGATCCAACTAGCGAGTCATCAT 59.994 47.826 6.95 0.00 33.58 2.45
3641 8245 1.207089 CACAAGAGCGGGATCCAACTA 59.793 52.381 15.23 0.00 0.00 2.24
3644 8248 0.250234 CTCACAAGAGCGGGATCCAA 59.750 55.000 15.23 0.00 34.61 3.53
3688 8298 0.673644 CTGCTCCCGATGTTTTCCGT 60.674 55.000 0.00 0.00 0.00 4.69
3866 8487 9.643693 AAAGCTCAACATTTTCCATGTAAATAG 57.356 29.630 0.00 0.63 0.00 1.73
3896 8517 3.921104 AGGGTATGAGAGATGAGCAAGA 58.079 45.455 0.00 0.00 0.00 3.02
3948 8569 2.358247 CCACCCCACTTTCGGACG 60.358 66.667 0.00 0.00 0.00 4.79
4044 8665 3.987868 TGATCAGTACAAAGACGAACAGC 59.012 43.478 0.00 0.00 0.00 4.40
4045 8666 4.982295 TGTGATCAGTACAAAGACGAACAG 59.018 41.667 0.00 0.00 0.00 3.16
4099 8720 3.264964 TCAACCTGGTTTCCATACCCTAC 59.735 47.826 9.90 0.00 37.39 3.18
4135 8756 5.010617 GGTTTCCACTATTCAGGCTCAAAAA 59.989 40.000 0.00 0.00 0.00 1.94
4136 8757 4.522789 GGTTTCCACTATTCAGGCTCAAAA 59.477 41.667 0.00 0.00 0.00 2.44
4137 8758 4.079253 GGTTTCCACTATTCAGGCTCAAA 58.921 43.478 0.00 0.00 0.00 2.69
4138 8759 3.073798 TGGTTTCCACTATTCAGGCTCAA 59.926 43.478 0.00 0.00 0.00 3.02
4139 8760 2.642311 TGGTTTCCACTATTCAGGCTCA 59.358 45.455 0.00 0.00 0.00 4.26
4140 8761 3.350219 TGGTTTCCACTATTCAGGCTC 57.650 47.619 0.00 0.00 0.00 4.70
4141 8762 4.141390 CCTATGGTTTCCACTATTCAGGCT 60.141 45.833 0.00 0.00 35.80 4.58
4142 8763 4.137543 CCTATGGTTTCCACTATTCAGGC 58.862 47.826 0.00 0.00 35.80 4.85
4143 8764 5.131142 ACTCCTATGGTTTCCACTATTCAGG 59.869 44.000 0.00 0.00 35.80 3.86
4144 8765 6.240549 ACTCCTATGGTTTCCACTATTCAG 57.759 41.667 0.00 0.00 35.80 3.02
4145 8766 7.931015 ATACTCCTATGGTTTCCACTATTCA 57.069 36.000 0.00 0.00 35.80 2.57
4146 8767 9.877178 CATATACTCCTATGGTTTCCACTATTC 57.123 37.037 0.00 0.00 35.80 1.75
4147 8768 9.393786 ACATATACTCCTATGGTTTCCACTATT 57.606 33.333 0.00 0.00 35.80 1.73
4148 8769 8.974292 ACATATACTCCTATGGTTTCCACTAT 57.026 34.615 0.00 0.00 35.80 2.12
4149 8770 8.232412 AGACATATACTCCTATGGTTTCCACTA 58.768 37.037 0.00 0.00 35.80 2.74
4150 8771 7.076446 AGACATATACTCCTATGGTTTCCACT 58.924 38.462 0.00 0.00 35.80 4.00
4151 8772 7.304497 AGACATATACTCCTATGGTTTCCAC 57.696 40.000 0.00 0.00 35.80 4.02
4152 8773 7.689313 GCAAGACATATACTCCTATGGTTTCCA 60.689 40.741 0.00 0.00 38.19 3.53
4153 8774 6.651225 GCAAGACATATACTCCTATGGTTTCC 59.349 42.308 0.00 0.00 34.11 3.13
4154 8775 7.217200 TGCAAGACATATACTCCTATGGTTTC 58.783 38.462 0.00 0.00 34.11 2.78
4155 8776 7.136822 TGCAAGACATATACTCCTATGGTTT 57.863 36.000 0.00 0.00 34.11 3.27
4156 8777 6.747414 TGCAAGACATATACTCCTATGGTT 57.253 37.500 0.00 0.00 34.11 3.67
4157 8778 6.350528 CGATGCAAGACATATACTCCTATGGT 60.351 42.308 0.00 0.00 39.84 3.55
4158 8779 6.038985 CGATGCAAGACATATACTCCTATGG 58.961 44.000 0.00 0.00 39.84 2.74
4159 8780 6.625362 ACGATGCAAGACATATACTCCTATG 58.375 40.000 0.00 0.00 39.84 2.23
4160 8781 6.842437 ACGATGCAAGACATATACTCCTAT 57.158 37.500 0.00 0.00 39.84 2.57
4161 8782 6.650427 AACGATGCAAGACATATACTCCTA 57.350 37.500 0.00 0.00 39.84 2.94
4162 8783 5.537300 AACGATGCAAGACATATACTCCT 57.463 39.130 0.00 0.00 39.84 3.69
4163 8784 7.090808 TCATAACGATGCAAGACATATACTCC 58.909 38.462 0.00 0.00 39.84 3.85
4164 8785 7.201393 GCTCATAACGATGCAAGACATATACTC 60.201 40.741 0.00 0.00 39.84 2.59
4165 8786 6.587990 GCTCATAACGATGCAAGACATATACT 59.412 38.462 0.00 0.00 39.84 2.12
4166 8787 6.183360 GGCTCATAACGATGCAAGACATATAC 60.183 42.308 0.00 0.00 39.84 1.47
4372 8995 9.839817 TTTCCCAAAAAGAAATACCCTAAAAAG 57.160 29.630 0.00 0.00 0.00 2.27
4395 9018 2.147436 TGCCGTTGAAGCCATTTTTC 57.853 45.000 0.00 0.00 0.00 2.29
4456 9101 0.697854 AATAGGCCCGTTCCCATCCT 60.698 55.000 0.00 0.00 0.00 3.24
4457 9102 0.537371 CAATAGGCCCGTTCCCATCC 60.537 60.000 0.00 0.00 0.00 3.51
4458 9103 0.537371 CCAATAGGCCCGTTCCCATC 60.537 60.000 0.00 0.00 0.00 3.51
4459 9104 0.991355 TCCAATAGGCCCGTTCCCAT 60.991 55.000 0.00 0.00 33.74 4.00
4460 9105 0.991355 ATCCAATAGGCCCGTTCCCA 60.991 55.000 0.00 0.00 33.74 4.37
4461 9106 1.061546 TATCCAATAGGCCCGTTCCC 58.938 55.000 0.00 0.00 33.74 3.97
4462 9107 2.943036 TTATCCAATAGGCCCGTTCC 57.057 50.000 0.00 0.00 33.74 3.62
4463 9108 3.949113 TGTTTTATCCAATAGGCCCGTTC 59.051 43.478 0.00 0.00 33.74 3.95
4464 9109 3.970842 TGTTTTATCCAATAGGCCCGTT 58.029 40.909 0.00 0.00 33.74 4.44
4465 9110 3.655615 TGTTTTATCCAATAGGCCCGT 57.344 42.857 0.00 0.00 33.74 5.28
4466 9111 3.697045 TGTTGTTTTATCCAATAGGCCCG 59.303 43.478 0.00 0.00 33.74 6.13
4467 9112 5.669164 TTGTTGTTTTATCCAATAGGCCC 57.331 39.130 0.00 0.00 33.74 5.80
4468 9113 8.474831 ACTAATTGTTGTTTTATCCAATAGGCC 58.525 33.333 0.00 0.00 33.74 5.19
4490 9135 5.570844 GCCTTTGACCCTCAGTGAATACTAA 60.571 44.000 0.00 0.00 34.74 2.24
4652 9313 7.573843 CGCAACATAGTTTTCTTCTCTCCAAAT 60.574 37.037 0.00 0.00 0.00 2.32
4694 9355 1.301401 TTGGCGGACTTCTTCACGG 60.301 57.895 0.00 0.00 0.00 4.94
4755 9416 1.593296 TTGTGTGTGCTGCTGTGCAA 61.593 50.000 0.00 0.00 45.12 4.08
4788 9449 3.181367 CTCACCAAGCACATCGGC 58.819 61.111 0.00 0.00 0.00 5.54
4949 9610 1.000163 CGAGTACACAGGCTGAGTTGT 60.000 52.381 23.66 17.42 0.00 3.32
4961 9622 2.243407 CAGTTTCTCGCTCGAGTACAC 58.757 52.381 15.13 12.56 42.49 2.90


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

AutoCloner maintained by Alex Coulton.