Multiple sequence alignment - TraesCS4B01G196100

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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 TraesCS4B01G196100 chr4B 100.000 5310 0 0 1 5310 422530964 422525655 0.000000e+00 9806.0
1 TraesCS4B01G196100 chr4B 97.826 92 2 0 4 95 422530870 422530961 5.500000e-35 159.0
2 TraesCS4B01G196100 chr4B 91.139 79 6 1 600 678 1994965 1994888 7.270000e-19 106.0
3 TraesCS4B01G196100 chr4B 76.471 187 34 7 4665 4848 28413271 28413092 5.660000e-15 93.5
4 TraesCS4B01G196100 chr4B 86.885 61 6 2 475 533 55782231 55782291 3.430000e-07 67.6
5 TraesCS4B01G196100 chr4D 96.184 3092 80 10 696 3775 341038409 341035344 0.000000e+00 5022.0
6 TraesCS4B01G196100 chr4D 93.356 888 52 5 4107 4988 341034880 341033994 0.000000e+00 1306.0
7 TraesCS4B01G196100 chr4D 89.095 486 31 6 90 553 341039473 341038988 7.660000e-163 584.0
8 TraesCS4B01G196100 chr4D 89.286 224 24 0 5004 5227 341033001 341032778 1.130000e-71 281.0
9 TraesCS4B01G196100 chr4D 74.630 473 102 12 4785 5248 95500557 95500094 5.430000e-45 193.0
10 TraesCS4B01G196100 chr4D 84.456 193 21 6 3775 3966 341035236 341035052 1.170000e-41 182.0
11 TraesCS4B01G196100 chr4D 90.110 91 5 3 590 678 85186272 85186184 1.210000e-21 115.0
12 TraesCS4B01G196100 chr4D 90.476 84 3 2 3998 4076 341034958 341034875 7.270000e-19 106.0
13 TraesCS4B01G196100 chr4A 96.060 2513 79 8 1270 3772 126414903 126417405 0.000000e+00 4074.0
14 TraesCS4B01G196100 chr4A 91.262 824 37 13 3775 4574 126417516 126418328 0.000000e+00 1090.0
15 TraesCS4B01G196100 chr4A 95.946 444 15 3 754 1197 126414136 126414576 0.000000e+00 717.0
16 TraesCS4B01G196100 chr4A 84.085 710 82 18 4574 5279 126418366 126419048 0.000000e+00 656.0
17 TraesCS4B01G196100 chr4A 89.825 285 23 2 269 553 126413830 126414108 1.410000e-95 361.0
18 TraesCS4B01G196100 chr4A 81.347 193 20 6 2575 2766 278427840 278427663 5.540000e-30 143.0
19 TraesCS4B01G196100 chr4A 80.412 194 21 8 2574 2766 403966495 403966318 1.200000e-26 132.0
20 TraesCS4B01G196100 chr4A 97.561 41 1 0 5270 5310 13582724 13582684 2.650000e-08 71.3
21 TraesCS4B01G196100 chr6A 76.336 655 130 17 4630 5266 116861780 116861133 1.430000e-85 327.0
22 TraesCS4B01G196100 chr6A 93.333 45 2 1 5266 5310 158050171 158050214 1.230000e-06 65.8
23 TraesCS4B01G196100 chr6D 75.877 684 131 17 4623 5275 471072890 471072210 8.580000e-83 318.0
24 TraesCS4B01G196100 chr6D 81.953 338 52 7 213 545 257954579 257954912 1.460000e-70 278.0
25 TraesCS4B01G196100 chr6D 77.305 141 25 6 4622 4759 12065674 12065538 5.700000e-10 76.8
26 TraesCS4B01G196100 chr2D 76.471 595 109 23 4702 5274 388057080 388057665 1.450000e-75 294.0
27 TraesCS4B01G196100 chr2D 73.139 618 137 16 4681 5275 608485318 608484707 1.510000e-45 195.0
28 TraesCS4B01G196100 chr2D 95.775 71 2 1 2697 2766 221044924 221044994 4.350000e-21 113.0
29 TraesCS4B01G196100 chr2D 95.349 43 2 0 5268 5310 623514850 623514892 9.540000e-08 69.4
30 TraesCS4B01G196100 chr5D 78.390 472 77 19 93 545 502700518 502700053 3.130000e-72 283.0
31 TraesCS4B01G196100 chr5D 73.865 639 129 22 4666 5275 42862874 42862245 2.490000e-53 220.0
32 TraesCS4B01G196100 chr5D 75.617 324 63 13 230 543 554335842 554335525 4.290000e-31 147.0
33 TraesCS4B01G196100 chr5D 94.937 79 3 1 600 678 513467332 513467255 7.220000e-24 122.0
34 TraesCS4B01G196100 chr5D 88.298 94 9 2 600 692 400605127 400605219 1.560000e-20 111.0
35 TraesCS4B01G196100 chr5D 85.714 84 10 2 4663 4745 14375609 14375527 2.630000e-13 87.9
36 TraesCS4B01G196100 chr2A 75.372 605 117 17 4661 5241 653004688 653005284 4.080000e-66 263.0
37 TraesCS4B01G196100 chr3B 78.030 396 80 7 4870 5261 812616206 812615814 5.310000e-60 243.0
38 TraesCS4B01G196100 chr3B 80.719 306 55 4 4962 5265 172725065 172724762 8.890000e-58 235.0
39 TraesCS4B01G196100 chr3B 96.842 95 2 1 7 100 683391963 683392057 1.980000e-34 158.0
40 TraesCS4B01G196100 chr3B 82.143 112 12 6 4664 4771 322283381 322283488 7.320000e-14 89.8
41 TraesCS4B01G196100 chr3D 76.447 501 85 18 4785 5277 463681990 463681515 1.910000e-59 241.0
42 TraesCS4B01G196100 chr3D 86.792 106 8 6 600 704 579731255 579731355 4.350000e-21 113.0
43 TraesCS4B01G196100 chr3D 73.054 334 64 22 4800 5115 267983455 267983780 1.570000e-15 95.3
44 TraesCS4B01G196100 chr3D 97.436 39 1 0 5270 5308 512678779 512678817 3.430000e-07 67.6
45 TraesCS4B01G196100 chrUn 80.921 304 56 2 4962 5264 68800937 68801239 6.870000e-59 239.0
46 TraesCS4B01G196100 chrUn 98.876 89 1 0 7 95 279936300 279936212 5.500000e-35 159.0
47 TraesCS4B01G196100 chrUn 98.876 89 1 0 7 95 395541687 395541599 5.500000e-35 159.0
48 TraesCS4B01G196100 chrUn 97.436 39 1 0 5272 5310 369790578 369790616 3.430000e-07 67.6
49 TraesCS4B01G196100 chrUn 97.436 39 1 0 5272 5310 434534497 434534535 3.430000e-07 67.6
50 TraesCS4B01G196100 chr1D 84.656 189 14 2 2575 2763 421382042 421381869 1.970000e-39 174.0
51 TraesCS4B01G196100 chr1D 76.176 340 65 12 213 543 62220872 62220540 1.180000e-36 165.0
52 TraesCS4B01G196100 chr1D 75.229 218 39 8 5094 5310 57313485 57313282 7.320000e-14 89.8
53 TraesCS4B01G196100 chr2B 76.415 318 69 4 233 545 33346732 33346416 3.290000e-37 167.0
54 TraesCS4B01G196100 chr2B 91.379 116 9 1 5 120 54765905 54766019 1.980000e-34 158.0
55 TraesCS4B01G196100 chr2B 97.701 87 2 0 7 93 785216337 785216423 3.310000e-32 150.0
56 TraesCS4B01G196100 chr2B 78.109 201 35 6 5037 5237 19082628 19082819 9.340000e-23 119.0
57 TraesCS4B01G196100 chr2B 88.421 95 9 2 599 692 509057592 509057685 4.350000e-21 113.0
58 TraesCS4B01G196100 chr2B 73.750 320 59 21 4827 5137 41385126 41384823 9.410000e-18 102.0
59 TraesCS4B01G196100 chr2B 97.674 43 0 1 5269 5310 708438559 708438517 7.380000e-09 73.1
60 TraesCS4B01G196100 chr7B 100.000 88 0 0 6 93 64651078 64651165 4.260000e-36 163.0
61 TraesCS4B01G196100 chr7B 88.298 94 9 2 600 692 734117166 734117074 1.560000e-20 111.0
62 TraesCS4B01G196100 chr7B 87.500 96 9 3 590 684 157681672 157681765 2.020000e-19 108.0
63 TraesCS4B01G196100 chr7D 95.833 96 4 0 6 101 146660436 146660341 7.120000e-34 156.0
64 TraesCS4B01G196100 chr7A 94.949 99 5 0 4 102 549354519 549354617 7.120000e-34 156.0
65 TraesCS4B01G196100 chr7A 86.154 130 16 2 2362 2489 399043480 399043351 7.170000e-29 139.0
66 TraesCS4B01G196100 chr7A 84.127 126 18 2 2366 2489 505565632 505565507 2.600000e-23 121.0
67 TraesCS4B01G196100 chr1B 88.298 94 7 4 600 691 249511498 249511589 5.620000e-20 110.0
68 TraesCS4B01G196100 chr5B 87.342 79 8 2 4784 4862 42228184 42228108 7.320000e-14 89.8
69 TraesCS4B01G196100 chr5B 100.000 36 0 0 5275 5310 543268708 543268673 3.430000e-07 67.6
70 TraesCS4B01G196100 chr5A 83.951 81 8 5 460 537 411992566 411992644 7.380000e-09 73.1


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 TraesCS4B01G196100 chr4B 422525655 422530964 5309 True 9806.000000 9806 100.0000 1 5310 1 chr4B.!!$R3 5309
1 TraesCS4B01G196100 chr4D 341032778 341039473 6695 True 1246.833333 5022 90.4755 90 5227 6 chr4D.!!$R3 5137
2 TraesCS4B01G196100 chr4A 126413830 126419048 5218 False 1379.600000 4074 91.4356 269 5279 5 chr4A.!!$F1 5010
3 TraesCS4B01G196100 chr6A 116861133 116861780 647 True 327.000000 327 76.3360 4630 5266 1 chr6A.!!$R1 636
4 TraesCS4B01G196100 chr6D 471072210 471072890 680 True 318.000000 318 75.8770 4623 5275 1 chr6D.!!$R2 652
5 TraesCS4B01G196100 chr2D 388057080 388057665 585 False 294.000000 294 76.4710 4702 5274 1 chr2D.!!$F2 572
6 TraesCS4B01G196100 chr5D 42862245 42862874 629 True 220.000000 220 73.8650 4666 5275 1 chr5D.!!$R2 609
7 TraesCS4B01G196100 chr2A 653004688 653005284 596 False 263.000000 263 75.3720 4661 5241 1 chr2A.!!$F1 580

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
19 20 0.108945 CGGTTGTACTCCCTCCGTTC 60.109 60.000 0.0 0.0 36.99 3.95 F
1220 1686 0.107165 GCCTGAATCTACACCCCCAC 60.107 60.000 0.0 0.0 0.00 4.61 F
1223 1689 0.120377 TGAATCTACACCCCCACCCT 59.880 55.000 0.0 0.0 0.00 4.34 F
1330 2050 0.839946 CTGTTATCACAGGGAGGGGG 59.160 60.000 0.0 0.0 46.10 5.40 F
1382 2102 1.522355 CCATGGCTGCTGTCGGTAG 60.522 63.158 0.0 0.0 0.00 3.18 F
1717 2444 2.032681 GCCAGCGTTCTTCAGGGT 59.967 61.111 0.0 0.0 0.00 4.34 F
3079 3809 0.321122 GCTTGCTGCCACAGAGTAGT 60.321 55.000 0.0 0.0 32.44 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 2595 0.108585 TTGGCTCTGAGGGTGTTGAC 59.891 55.000 6.83 0.0 0.00 3.18 R
2396 3123 1.291184 TGTTTCGCCACTGCTCGATG 61.291 55.000 0.00 0.0 34.48 3.84 R
2444 3171 2.192664 TTTCAACAAGCGGGCTCATA 57.807 45.000 0.00 0.0 0.00 2.15 R
2825 3552 2.834689 CGCAAGTTGATGGAAACGTAC 58.165 47.619 7.16 0.0 35.13 3.67 R
3079 3809 4.081917 TGAACAGTATAATCAGCACGGACA 60.082 41.667 0.00 0.0 0.00 4.02 R
3549 4280 0.674895 CCACAGCCAGTACAAGAGCC 60.675 60.000 0.00 0.0 0.00 4.70 R
4924 5905 0.110486 ACAAGCACGGACCAAATCCT 59.890 50.000 0.00 0.0 46.69 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.690745 CGGTTGTACTCCCTCCGT 58.309 61.111 0.00 0.00 36.99 4.69
18 19 1.969862 CGGTTGTACTCCCTCCGTT 59.030 57.895 0.00 0.00 36.99 4.44
19 20 0.108945 CGGTTGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 36.99 3.95
20 21 0.248565 GGTTGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
21 22 0.971386 GTTGTACTCCCTCCGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
22 23 1.345415 GTTGTACTCCCTCCGTTCCAA 59.655 52.381 0.00 0.00 0.00 3.53
23 24 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
24 25 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
25 26 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
26 27 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
27 28 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
28 29 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
29 30 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
30 31 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
31 32 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
32 33 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
33 34 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
34 35 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
35 36 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
36 37 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
37 38 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
38 39 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
39 40 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
40 41 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
41 42 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
42 43 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
43 44 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
44 45 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
45 46 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
49 50 9.877178 AATAGATGACTCAACTTTGTACTAAGG 57.123 33.333 19.08 5.92 0.00 2.69
50 51 7.304497 AGATGACTCAACTTTGTACTAAGGT 57.696 36.000 19.08 11.48 0.00 3.50
51 52 7.736893 AGATGACTCAACTTTGTACTAAGGTT 58.263 34.615 19.08 9.89 0.00 3.50
52 53 8.867097 AGATGACTCAACTTTGTACTAAGGTTA 58.133 33.333 19.08 5.55 0.00 2.85
53 54 9.141400 GATGACTCAACTTTGTACTAAGGTTAG 57.859 37.037 19.08 15.84 36.82 2.34
54 55 8.015185 TGACTCAACTTTGTACTAAGGTTAGT 57.985 34.615 17.99 17.99 45.39 2.24
55 56 9.135189 TGACTCAACTTTGTACTAAGGTTAGTA 57.865 33.333 17.97 5.64 43.36 1.82
68 69 8.015185 ACTAAGGTTAGTACAAAGTTGAGTCA 57.985 34.615 0.32 0.00 41.92 3.41
69 70 8.648693 ACTAAGGTTAGTACAAAGTTGAGTCAT 58.351 33.333 0.32 0.00 41.92 3.06
70 71 7.964604 AAGGTTAGTACAAAGTTGAGTCATC 57.035 36.000 0.00 0.00 0.00 2.92
71 72 7.304497 AGGTTAGTACAAAGTTGAGTCATCT 57.696 36.000 0.00 0.00 0.00 2.90
72 73 8.418597 AGGTTAGTACAAAGTTGAGTCATCTA 57.581 34.615 4.14 0.00 0.00 1.98
73 74 9.036980 AGGTTAGTACAAAGTTGAGTCATCTAT 57.963 33.333 4.14 0.00 0.00 1.98
74 75 9.654663 GGTTAGTACAAAGTTGAGTCATCTATT 57.345 33.333 4.14 0.00 0.00 1.73
78 79 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
79 80 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
80 81 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
81 82 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
82 83 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
83 84 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
84 85 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
85 86 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
86 87 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
87 88 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
88 89 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
101 102 2.236395 ACGGAGGGAGTACAATCAAAGG 59.764 50.000 0.00 0.00 0.00 3.11
121 122 1.956170 CCTATCCGTCGCATGGTGC 60.956 63.158 0.00 0.00 40.69 5.01
179 180 9.148104 ACATTAAGAGTTTAACGAATACACCTC 57.852 33.333 0.00 0.00 31.90 3.85
202 203 8.106462 CCTCTTGTATCTACAGAGATAGGATCA 58.894 40.741 13.65 0.00 43.84 2.92
241 264 0.620556 CTTTGCCCTTAGCCTCTCCA 59.379 55.000 0.00 0.00 42.71 3.86
252 275 1.670590 CCTCTCCATGGCTCGATCC 59.329 63.158 6.96 0.00 0.00 3.36
307 330 6.834959 TTGCGAATGAGATAAGAGACAATC 57.165 37.500 0.00 0.00 0.00 2.67
380 403 4.561500 TTCCTCCAACAAATACATCGGA 57.438 40.909 0.00 0.00 0.00 4.55
384 407 4.640201 CCTCCAACAAATACATCGGATTGT 59.360 41.667 0.00 0.00 37.59 2.71
388 411 5.008613 CCAACAAATACATCGGATTGTAGGG 59.991 44.000 0.00 0.00 35.65 3.53
401 424 4.141711 GGATTGTAGGGCTATGTCTCAACA 60.142 45.833 0.00 0.00 40.38 3.33
424 447 4.525487 ACATGACCTTACCGAACTACTCAA 59.475 41.667 0.00 0.00 0.00 3.02
483 506 8.542497 AAAAACACATCATGAAGATTGATTGG 57.458 30.769 4.68 0.00 33.72 3.16
513 536 6.817765 ATATGTCTTACAATAATTGCGGGG 57.182 37.500 0.00 0.00 0.00 5.73
553 576 8.863872 ACAAAGTATGGCTAGTTAGAAATGTT 57.136 30.769 0.00 0.00 0.00 2.71
554 577 9.297037 ACAAAGTATGGCTAGTTAGAAATGTTT 57.703 29.630 0.00 0.00 0.00 2.83
557 580 7.762382 AGTATGGCTAGTTAGAAATGTTTTGC 58.238 34.615 0.00 0.00 0.00 3.68
558 581 5.385509 TGGCTAGTTAGAAATGTTTTGCC 57.614 39.130 0.00 0.00 37.38 4.52
559 582 4.219725 TGGCTAGTTAGAAATGTTTTGCCC 59.780 41.667 0.00 0.00 36.17 5.36
560 583 4.381612 GGCTAGTTAGAAATGTTTTGCCCC 60.382 45.833 0.00 0.00 0.00 5.80
561 584 4.381612 GCTAGTTAGAAATGTTTTGCCCCC 60.382 45.833 0.00 0.00 0.00 5.40
583 606 6.980397 CCCCCTTTAATTTCGAAGATTGATTG 59.020 38.462 12.75 4.80 35.04 2.67
586 609 9.807649 CCCTTTAATTTCGAAGATTGATTGATT 57.192 29.630 12.75 4.27 35.04 2.57
603 626 9.739276 TTGATTGATTGATATTATGGTACCCTC 57.261 33.333 10.07 0.00 0.00 4.30
605 628 6.294361 TGATTGATATTATGGTACCCTCCG 57.706 41.667 10.07 0.00 0.00 4.63
606 629 5.783360 TGATTGATATTATGGTACCCTCCGT 59.217 40.000 10.07 0.00 0.00 4.69
608 631 4.091549 TGATATTATGGTACCCTCCGTCC 58.908 47.826 10.07 0.00 0.00 4.79
611 634 0.564171 TATGGTACCCTCCGTCCCAT 59.436 55.000 10.07 0.00 39.22 4.00
612 635 0.564171 ATGGTACCCTCCGTCCCATA 59.436 55.000 10.07 0.00 34.22 2.74
613 636 0.339162 TGGTACCCTCCGTCCCATAA 59.661 55.000 10.07 0.00 0.00 1.90
615 638 2.179645 TGGTACCCTCCGTCCCATAATA 59.820 50.000 10.07 0.00 0.00 0.98
616 639 3.181404 TGGTACCCTCCGTCCCATAATAT 60.181 47.826 10.07 0.00 0.00 1.28
617 640 4.045718 TGGTACCCTCCGTCCCATAATATA 59.954 45.833 10.07 0.00 0.00 0.86
618 641 5.025453 GGTACCCTCCGTCCCATAATATAA 58.975 45.833 0.00 0.00 0.00 0.98
619 642 5.128335 GGTACCCTCCGTCCCATAATATAAG 59.872 48.000 0.00 0.00 0.00 1.73
620 643 5.019657 ACCCTCCGTCCCATAATATAAGA 57.980 43.478 0.00 0.00 0.00 2.10
621 644 5.408824 ACCCTCCGTCCCATAATATAAGAA 58.591 41.667 0.00 0.00 0.00 2.52
622 645 5.247792 ACCCTCCGTCCCATAATATAAGAAC 59.752 44.000 0.00 0.00 0.00 3.01
624 647 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
625 648 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
626 649 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
629 652 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
630 653 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
631 654 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
675 856 9.681062 AAACGTTATTATATTATGGGATGGAGG 57.319 33.333 0.00 0.00 0.00 4.30
676 857 7.802117 ACGTTATTATATTATGGGATGGAGGG 58.198 38.462 0.00 0.00 0.00 4.30
677 858 7.626084 ACGTTATTATATTATGGGATGGAGGGA 59.374 37.037 0.00 0.00 0.00 4.20
680 861 6.891306 TTATATTATGGGATGGAGGGACTG 57.109 41.667 0.00 0.00 41.55 3.51
740 1199 0.885196 AAAACAAGGTGTGTGCACGT 59.115 45.000 13.13 0.00 46.13 4.49
741 1200 0.170116 AAACAAGGTGTGTGCACGTG 59.830 50.000 12.28 12.28 46.13 4.49
742 1201 0.958382 AACAAGGTGTGTGCACGTGT 60.958 50.000 18.38 6.34 46.13 4.49
743 1202 1.351707 CAAGGTGTGTGCACGTGTC 59.648 57.895 18.38 10.14 46.13 3.67
744 1203 1.089481 CAAGGTGTGTGCACGTGTCT 61.089 55.000 18.38 4.59 46.13 3.41
745 1204 0.392461 AAGGTGTGTGCACGTGTCTT 60.392 50.000 18.38 10.49 46.13 3.01
875 1334 0.547471 CCCCAATTTGCCTCCCCTTT 60.547 55.000 0.00 0.00 0.00 3.11
877 1336 2.545810 CCCAATTTGCCTCCCCTTTAA 58.454 47.619 0.00 0.00 0.00 1.52
880 1339 4.018506 CCCAATTTGCCTCCCCTTTAATTT 60.019 41.667 0.00 0.00 0.00 1.82
881 1340 5.185454 CCAATTTGCCTCCCCTTTAATTTC 58.815 41.667 0.00 0.00 0.00 2.17
882 1341 4.736126 ATTTGCCTCCCCTTTAATTTCG 57.264 40.909 0.00 0.00 0.00 3.46
884 1343 3.443145 TGCCTCCCCTTTAATTTCGAA 57.557 42.857 0.00 0.00 0.00 3.71
887 1346 3.021695 CCTCCCCTTTAATTTCGAACCC 58.978 50.000 0.00 0.00 0.00 4.11
888 1347 3.562609 CCTCCCCTTTAATTTCGAACCCA 60.563 47.826 0.00 0.00 0.00 4.51
937 1403 4.767255 CCCTGTCGCTGCAGACCC 62.767 72.222 20.43 3.78 40.26 4.46
1156 1622 3.423162 CTCCTCCTTGCGCTCTCCG 62.423 68.421 9.73 0.00 40.75 4.63
1208 1674 0.974010 TCGTCCCGGTAAGCCTGAAT 60.974 55.000 0.00 0.00 0.00 2.57
1209 1675 0.529992 CGTCCCGGTAAGCCTGAATC 60.530 60.000 0.00 0.00 0.00 2.52
1210 1676 0.831307 GTCCCGGTAAGCCTGAATCT 59.169 55.000 0.00 0.00 0.00 2.40
1211 1677 2.037144 GTCCCGGTAAGCCTGAATCTA 58.963 52.381 0.00 0.00 0.00 1.98
1212 1678 2.037144 TCCCGGTAAGCCTGAATCTAC 58.963 52.381 0.00 0.00 0.00 2.59
1213 1679 1.760613 CCCGGTAAGCCTGAATCTACA 59.239 52.381 0.00 0.00 0.00 2.74
1214 1680 2.483188 CCCGGTAAGCCTGAATCTACAC 60.483 54.545 0.00 0.00 0.00 2.90
1215 1681 2.483188 CCGGTAAGCCTGAATCTACACC 60.483 54.545 0.00 0.00 0.00 4.16
1216 1682 2.483188 CGGTAAGCCTGAATCTACACCC 60.483 54.545 0.00 0.00 0.00 4.61
1217 1683 2.158798 GGTAAGCCTGAATCTACACCCC 60.159 54.545 0.00 0.00 0.00 4.95
1218 1684 0.919710 AAGCCTGAATCTACACCCCC 59.080 55.000 0.00 0.00 0.00 5.40
1219 1685 0.253160 AGCCTGAATCTACACCCCCA 60.253 55.000 0.00 0.00 0.00 4.96
1220 1686 0.107165 GCCTGAATCTACACCCCCAC 60.107 60.000 0.00 0.00 0.00 4.61
1221 1687 0.546598 CCTGAATCTACACCCCCACC 59.453 60.000 0.00 0.00 0.00 4.61
1222 1688 0.546598 CTGAATCTACACCCCCACCC 59.453 60.000 0.00 0.00 0.00 4.61
1223 1689 0.120377 TGAATCTACACCCCCACCCT 59.880 55.000 0.00 0.00 0.00 4.34
1285 2005 6.078456 TGAACCCCAGATCATTAGTTCATT 57.922 37.500 13.93 0.00 38.82 2.57
1290 2010 6.828785 ACCCCAGATCATTAGTTCATTACAAC 59.171 38.462 0.00 0.00 0.00 3.32
1295 2015 5.849357 TCATTAGTTCATTACAACGCGTT 57.151 34.783 20.79 20.79 0.00 4.84
1330 2050 0.839946 CTGTTATCACAGGGAGGGGG 59.160 60.000 0.00 0.00 46.10 5.40
1382 2102 1.522355 CCATGGCTGCTGTCGGTAG 60.522 63.158 0.00 0.00 0.00 3.18
1386 2106 2.352032 GGCTGCTGTCGGTAGGTCT 61.352 63.158 0.00 0.00 0.00 3.85
1422 2149 4.562789 GCTAGATTGGGCGTTTTGAAAATC 59.437 41.667 0.00 0.00 0.00 2.17
1586 2313 8.976471 GTAAAACTTGACACTCTTAGGTCTTAC 58.024 37.037 0.00 0.00 35.11 2.34
1616 2343 3.643199 TTGTTGTGCCAGATATGCCTA 57.357 42.857 0.00 0.00 0.00 3.93
1629 2356 8.197439 GCCAGATATGCCTACAAAATTTAACTT 58.803 33.333 0.00 0.00 0.00 2.66
1717 2444 2.032681 GCCAGCGTTCTTCAGGGT 59.967 61.111 0.00 0.00 0.00 4.34
2396 3123 2.674796 GTCTGGGTGTGTATCCTGAC 57.325 55.000 0.00 0.00 45.15 3.51
2444 3171 2.224402 GCAGTGGTTCTCTTCAGTCCTT 60.224 50.000 0.00 0.00 0.00 3.36
2651 3378 3.869272 GCGATCTGCCAAGCACGG 61.869 66.667 0.00 0.00 37.76 4.94
2825 3552 2.989840 CCTGCTTAGTCTTGTCTGTTCG 59.010 50.000 0.00 0.00 0.00 3.95
2916 3644 4.568760 GCATGAACTTCCTGACTTACTAGC 59.431 45.833 0.00 0.00 0.00 3.42
2986 3716 2.548547 AAACCCCCTCCTTCCAGCC 61.549 63.158 0.00 0.00 0.00 4.85
3079 3809 0.321122 GCTTGCTGCCACAGAGTAGT 60.321 55.000 0.00 0.00 32.44 2.73
3360 4091 0.533755 AGCTGCCAACTGACTCACAC 60.534 55.000 0.00 0.00 0.00 3.82
3387 4118 5.590259 TCTTCTCTACTTGTTTGCTGCTTTT 59.410 36.000 0.00 0.00 0.00 2.27
3432 4163 5.688807 CTTCATGTTGATCCAACCTCCTAT 58.311 41.667 7.29 0.00 42.96 2.57
3549 4280 2.034124 CCAGCAATTATTCACCCAGGG 58.966 52.381 2.85 2.85 0.00 4.45
3586 4317 1.376466 GGCAAGCAGAGTCCTCCAA 59.624 57.895 0.00 0.00 0.00 3.53
3595 4326 3.006217 GCAGAGTCCTCCAATTTTTGCTT 59.994 43.478 0.00 0.00 0.00 3.91
3612 4343 7.589958 TTTTGCTTTATACTGGGACAAGAAA 57.410 32.000 0.00 0.00 38.70 2.52
3639 4370 6.091437 GCAATTTTCTCTTCAGGTGATTCAG 58.909 40.000 0.00 0.00 0.00 3.02
3651 4382 4.701651 CAGGTGATTCAGGCATTTCTGTTA 59.298 41.667 0.00 0.00 36.25 2.41
3653 4384 5.183904 AGGTGATTCAGGCATTTCTGTTAAC 59.816 40.000 0.00 0.00 36.25 2.01
3665 4396 8.819974 GGCATTTCTGTTAACCAATTAATCATG 58.180 33.333 2.48 0.00 32.91 3.07
3723 4454 9.697250 CAAATGTAATCATTGAACATGAATTGC 57.303 29.630 0.00 0.00 42.60 3.56
3738 4469 4.366586 TGAATTGCGAAATTGCTGAAACA 58.633 34.783 5.96 0.00 35.36 2.83
3767 4498 9.282247 GAGTTTAATAAGACATGCAACATTGAG 57.718 33.333 0.00 0.00 0.00 3.02
3772 4503 5.779529 AAGACATGCAACATTGAGAGTTT 57.220 34.783 0.00 0.00 0.00 2.66
3780 4619 8.857216 CATGCAACATTGAGAGTTTAATCTTTC 58.143 33.333 0.00 0.00 0.00 2.62
3790 4629 6.181190 AGAGTTTAATCTTTCTACCCCTTGC 58.819 40.000 0.00 0.00 0.00 4.01
3794 4633 2.038863 TCTTTCTACCCCTTGCCTGA 57.961 50.000 0.00 0.00 0.00 3.86
3795 4634 2.562296 TCTTTCTACCCCTTGCCTGAT 58.438 47.619 0.00 0.00 0.00 2.90
3801 4640 3.785887 TCTACCCCTTGCCTGATTGTATT 59.214 43.478 0.00 0.00 0.00 1.89
3810 4649 4.148079 TGCCTGATTGTATTTTGGTGTGA 58.852 39.130 0.00 0.00 0.00 3.58
3812 4651 4.923281 GCCTGATTGTATTTTGGTGTGAAC 59.077 41.667 0.00 0.00 0.00 3.18
3822 4661 4.582701 TTTGGTGTGAACATGGTGAATC 57.417 40.909 0.00 0.00 0.00 2.52
3830 4669 7.362834 GGTGTGAACATGGTGAATCATGATAAA 60.363 37.037 9.04 0.00 45.30 1.40
3833 4672 9.590451 GTGAACATGGTGAATCATGATAAAAAT 57.410 29.630 9.04 0.00 45.30 1.82
3861 4701 7.744087 TGGTATATAGCATGATTTTGACACC 57.256 36.000 10.55 0.00 0.00 4.16
3866 4706 3.937814 AGCATGATTTTGACACCGAGTA 58.062 40.909 0.00 0.00 0.00 2.59
3872 4712 5.120399 TGATTTTGACACCGAGTAGTTTGT 58.880 37.500 0.00 0.00 0.00 2.83
3879 4719 2.217847 CACCGAGTAGTTTGTTGTGACG 59.782 50.000 0.00 0.00 0.00 4.35
3974 4815 5.806654 TGCATAGAGGTATACATCAAGCA 57.193 39.130 18.93 19.63 31.46 3.91
4096 5004 5.519927 AGTTGCTTGCAAAATGTTGTTACTC 59.480 36.000 9.75 0.00 37.06 2.59
4159 5068 7.901874 ATTAATGTTGTACACACGTGTTTTC 57.098 32.000 20.79 11.68 41.83 2.29
4347 5256 2.353406 CGTCGGGAGGAAACTGTTGTAT 60.353 50.000 0.00 0.00 44.43 2.29
4350 5259 4.069304 TCGGGAGGAAACTGTTGTATTTG 58.931 43.478 0.00 0.00 44.43 2.32
4351 5260 3.818773 CGGGAGGAAACTGTTGTATTTGT 59.181 43.478 0.00 0.00 44.43 2.83
4352 5261 4.998672 CGGGAGGAAACTGTTGTATTTGTA 59.001 41.667 0.00 0.00 44.43 2.41
4353 5262 5.106830 CGGGAGGAAACTGTTGTATTTGTAC 60.107 44.000 0.00 0.00 44.43 2.90
4511 5422 6.903883 TTCTGAGTTGTATCTTAAATCGCC 57.096 37.500 0.00 0.00 0.00 5.54
4844 5819 6.642950 CGGCGACTTCTTGAAGATAGAATAAT 59.357 38.462 16.21 0.00 31.66 1.28
4863 5841 1.267121 TGTTCTCACCTAGCCCTCAC 58.733 55.000 0.00 0.00 0.00 3.51
4885 5863 2.291465 CCCAACGGTGCATCTCATATTG 59.709 50.000 0.00 0.00 0.00 1.90
4886 5864 2.945008 CCAACGGTGCATCTCATATTGT 59.055 45.455 0.00 0.00 0.00 2.71
4924 5905 2.232941 GGTGTCTTCGGTGGATCTTGTA 59.767 50.000 0.00 0.00 0.00 2.41
4946 5927 2.614481 GGATTTGGTCCGTGCTTGTCTA 60.614 50.000 0.00 0.00 37.23 2.59
4990 5972 8.021973 TCTAGTCTTTGTTCTTCTACGTTCATC 58.978 37.037 0.00 0.00 0.00 2.92
4995 5977 4.806330 TGTTCTTCTACGTTCATCTGTCC 58.194 43.478 0.00 0.00 0.00 4.02
5007 6966 6.098409 ACGTTCATCTGTCCATAGGTTAGATT 59.902 38.462 0.00 0.00 29.42 2.40
5016 6975 8.473358 TGTCCATAGGTTAGATTCTTTCGATA 57.527 34.615 0.00 0.00 0.00 2.92
5020 6979 9.765795 CCATAGGTTAGATTCTTTCGATAAACT 57.234 33.333 0.00 0.00 0.00 2.66
5191 7153 1.731424 GCTTGTAGTCGTCGCTTGCTA 60.731 52.381 0.00 0.00 0.00 3.49
5305 7270 9.591792 TCAGTTTGTCTAATTCACATCTAGATG 57.408 33.333 27.63 27.63 44.15 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.248565 GGAACGGAGGGAGTACAACC 59.751 60.000 0.00 0.00 0.00 3.77
2 3 0.971386 TGGAACGGAGGGAGTACAAC 59.029 55.000 0.00 0.00 0.00 3.32
3 4 1.719529 TTGGAACGGAGGGAGTACAA 58.280 50.000 0.00 0.00 0.00 2.41
5 6 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
6 7 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
7 8 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
8 9 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
9 10 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
10 11 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
11 12 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
12 13 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
13 14 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
14 15 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
15 16 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
16 17 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
17 18 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
18 19 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
19 20 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
23 24 9.877178 CCTTAGTACAAAGTTGAGTCATCTATT 57.123 33.333 4.14 0.00 0.00 1.73
24 25 9.036980 ACCTTAGTACAAAGTTGAGTCATCTAT 57.963 33.333 4.14 0.00 0.00 1.98
25 26 8.418597 ACCTTAGTACAAAGTTGAGTCATCTA 57.581 34.615 4.14 0.00 0.00 1.98
26 27 7.304497 ACCTTAGTACAAAGTTGAGTCATCT 57.696 36.000 0.00 0.00 0.00 2.90
27 28 7.964604 AACCTTAGTACAAAGTTGAGTCATC 57.035 36.000 0.00 0.00 0.00 2.92
28 29 8.648693 ACTAACCTTAGTACAAAGTTGAGTCAT 58.351 33.333 0.00 0.00 41.92 3.06
29 30 8.015185 ACTAACCTTAGTACAAAGTTGAGTCA 57.985 34.615 0.00 0.00 41.92 3.41
42 43 9.135189 TGACTCAACTTTGTACTAACCTTAGTA 57.865 33.333 1.45 1.45 43.36 1.82
43 44 8.015185 TGACTCAACTTTGTACTAACCTTAGT 57.985 34.615 3.29 3.29 45.39 2.24
44 45 9.141400 GATGACTCAACTTTGTACTAACCTTAG 57.859 37.037 0.00 0.00 36.82 2.18
45 46 8.867097 AGATGACTCAACTTTGTACTAACCTTA 58.133 33.333 0.00 0.00 0.00 2.69
46 47 7.736893 AGATGACTCAACTTTGTACTAACCTT 58.263 34.615 0.00 0.00 0.00 3.50
47 48 7.304497 AGATGACTCAACTTTGTACTAACCT 57.696 36.000 0.00 0.00 0.00 3.50
48 49 9.654663 AATAGATGACTCAACTTTGTACTAACC 57.345 33.333 0.00 0.00 0.00 2.85
52 53 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
53 54 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
54 55 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
55 56 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
56 57 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
57 58 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
58 59 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
59 60 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
60 61 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
61 62 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
62 63 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
63 64 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
64 65 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
65 66 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
66 67 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
67 68 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
68 69 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
69 70 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
70 71 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
71 72 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
72 73 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
73 74 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
74 75 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
75 76 1.719529 TTGTACTCCCTCCGTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
76 77 1.829222 GATTGTACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
77 78 1.829222 TGATTGTACTCCCTCCGTTCC 59.171 52.381 0.00 0.00 0.00 3.62
78 79 3.604875 TTGATTGTACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
79 80 3.307480 CCTTTGATTGTACTCCCTCCGTT 60.307 47.826 0.00 0.00 0.00 4.44
80 81 2.236395 CCTTTGATTGTACTCCCTCCGT 59.764 50.000 0.00 0.00 0.00 4.69
81 82 2.906354 CCTTTGATTGTACTCCCTCCG 58.094 52.381 0.00 0.00 0.00 4.63
82 83 2.644676 GCCTTTGATTGTACTCCCTCC 58.355 52.381 0.00 0.00 0.00 4.30
83 84 2.644676 GGCCTTTGATTGTACTCCCTC 58.355 52.381 0.00 0.00 0.00 4.30
84 85 1.285078 GGGCCTTTGATTGTACTCCCT 59.715 52.381 0.84 0.00 0.00 4.20
85 86 1.285078 AGGGCCTTTGATTGTACTCCC 59.715 52.381 0.00 0.00 0.00 4.30
86 87 2.808906 AGGGCCTTTGATTGTACTCC 57.191 50.000 0.00 0.00 0.00 3.85
87 88 4.390264 GGATAGGGCCTTTGATTGTACTC 58.610 47.826 13.45 0.00 0.00 2.59
88 89 3.181454 CGGATAGGGCCTTTGATTGTACT 60.181 47.826 13.45 0.00 0.00 2.73
101 102 2.357517 CCATGCGACGGATAGGGC 60.358 66.667 0.09 0.00 0.00 5.19
121 122 8.417106 TCTGACTTATCTTAATTACTGAGGCAG 58.583 37.037 8.92 8.92 39.73 4.85
158 159 7.215085 ACAAGAGGTGTATTCGTTAAACTCTT 58.785 34.615 0.00 0.00 39.29 2.85
159 160 6.756221 ACAAGAGGTGTATTCGTTAAACTCT 58.244 36.000 0.00 0.00 39.29 3.24
188 189 9.264653 TGATAATAGCATTGATCCTATCTCTGT 57.735 33.333 0.00 0.00 0.00 3.41
202 203 6.201806 GCAAAGAGAGTCGTGATAATAGCATT 59.798 38.462 0.00 0.00 0.00 3.56
204 205 5.043903 GCAAAGAGAGTCGTGATAATAGCA 58.956 41.667 0.00 0.00 0.00 3.49
209 210 2.832129 AGGGCAAAGAGAGTCGTGATAA 59.168 45.455 0.00 0.00 0.00 1.75
241 264 0.683973 GATCACAGGGATCGAGCCAT 59.316 55.000 23.22 12.73 42.81 4.40
252 275 2.471815 TAGGTACCCAGGATCACAGG 57.528 55.000 8.74 0.00 0.00 4.00
272 295 4.081142 TCTCATTCGCAATCCTTGTCCTTA 60.081 41.667 0.00 0.00 0.00 2.69
380 403 4.225042 TGTGTTGAGACATAGCCCTACAAT 59.775 41.667 0.00 0.00 38.23 2.71
384 407 4.030216 TCATGTGTTGAGACATAGCCCTA 58.970 43.478 0.00 0.00 38.23 3.53
388 411 3.866651 AGGTCATGTGTTGAGACATAGC 58.133 45.455 0.00 0.00 38.23 2.97
401 424 4.084287 TGAGTAGTTCGGTAAGGTCATGT 58.916 43.478 0.00 0.00 0.00 3.21
505 528 1.817941 GTGTATCGCACCCCGCAAT 60.818 57.895 0.00 0.00 42.10 3.56
513 536 4.835199 ACTTTGTAATCGTGTATCGCAC 57.165 40.909 0.00 0.00 44.36 5.34
558 581 6.715347 ATCAATCTTCGAAATTAAAGGGGG 57.285 37.500 0.00 0.00 0.00 5.40
559 582 7.771183 TCAATCAATCTTCGAAATTAAAGGGG 58.229 34.615 0.00 0.00 0.00 4.79
560 583 9.807649 AATCAATCAATCTTCGAAATTAAAGGG 57.192 29.630 0.00 0.00 0.00 3.95
598 621 5.019657 TCTTATATTATGGGACGGAGGGT 57.980 43.478 0.00 0.00 0.00 4.34
599 622 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
602 625 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
603 626 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
605 628 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
606 629 8.605746 CGTCAAAAACGTTCTTATATTATGGGA 58.394 33.333 0.00 0.00 46.42 4.37
649 830 9.681062 CCTCCATCCCATAATATAATAACGTTT 57.319 33.333 5.91 0.00 0.00 3.60
656 837 6.126361 GCAGTCCCTCCATCCCATAATATAAT 60.126 42.308 0.00 0.00 0.00 1.28
661 842 1.707427 GCAGTCCCTCCATCCCATAAT 59.293 52.381 0.00 0.00 0.00 1.28
664 845 0.625683 AAGCAGTCCCTCCATCCCAT 60.626 55.000 0.00 0.00 0.00 4.00
665 846 1.229951 AAGCAGTCCCTCCATCCCA 60.230 57.895 0.00 0.00 0.00 4.37
666 847 1.225704 CAAGCAGTCCCTCCATCCC 59.774 63.158 0.00 0.00 0.00 3.85
668 849 2.206576 AAACAAGCAGTCCCTCCATC 57.793 50.000 0.00 0.00 0.00 3.51
670 851 3.806949 ATAAAACAAGCAGTCCCTCCA 57.193 42.857 0.00 0.00 0.00 3.86
671 852 5.468540 AAAATAAAACAAGCAGTCCCTCC 57.531 39.130 0.00 0.00 0.00 4.30
728 1187 0.580104 GTAAGACACGTGCACACACC 59.420 55.000 17.22 2.89 44.40 4.16
740 1199 3.002791 ACGAATCGGTACTCGTAAGACA 58.997 45.455 7.80 0.00 45.94 3.41
741 1200 3.665173 ACGAATCGGTACTCGTAAGAC 57.335 47.619 7.80 0.00 45.94 3.01
875 1334 4.901868 AGCTACACTTGGGTTCGAAATTA 58.098 39.130 0.00 0.00 0.00 1.40
877 1336 3.418684 AGCTACACTTGGGTTCGAAAT 57.581 42.857 0.00 0.00 0.00 2.17
880 1339 2.549349 GGAAAGCTACACTTGGGTTCGA 60.549 50.000 0.00 0.00 39.09 3.71
881 1340 1.804748 GGAAAGCTACACTTGGGTTCG 59.195 52.381 0.00 0.00 39.09 3.95
882 1341 3.141767 AGGAAAGCTACACTTGGGTTC 57.858 47.619 0.00 0.00 39.09 3.62
884 1343 4.929146 AATAGGAAAGCTACACTTGGGT 57.071 40.909 0.00 0.00 39.09 4.51
887 1346 7.648142 TGTTTGAAATAGGAAAGCTACACTTG 58.352 34.615 0.00 0.00 39.09 3.16
888 1347 7.522236 GCTGTTTGAAATAGGAAAGCTACACTT 60.522 37.037 3.88 0.00 41.70 3.16
1156 1622 1.575576 GATGAGGCAGATGCGATGGC 61.576 60.000 0.00 0.00 43.26 4.40
1208 1674 2.453054 GGAGGGTGGGGGTGTAGA 59.547 66.667 0.00 0.00 0.00 2.59
1209 1675 2.691252 GGGAGGGTGGGGGTGTAG 60.691 72.222 0.00 0.00 0.00 2.74
1210 1676 4.358181 GGGGAGGGTGGGGGTGTA 62.358 72.222 0.00 0.00 0.00 2.90
1285 2005 1.210870 GTGAGAACCAACGCGTTGTA 58.789 50.000 40.30 21.50 38.85 2.41
1290 2010 2.142418 GACACGTGAGAACCAACGCG 62.142 60.000 25.01 3.53 43.96 6.01
1295 2015 1.299850 CAGCGACACGTGAGAACCA 60.300 57.895 25.01 0.00 0.00 3.67
1330 2050 0.739112 CCAGCGACCTTGAAGAGCTC 60.739 60.000 5.27 5.27 35.82 4.09
1382 2102 2.977772 AGCATAGAGACAAGCAGACC 57.022 50.000 0.00 0.00 0.00 3.85
1449 2176 1.609208 ACACCTCATGAGCAACCAAC 58.391 50.000 17.76 0.00 0.00 3.77
1586 2313 2.798283 CTGGCACAACAAAGCATCTTTG 59.202 45.455 15.40 15.40 38.70 2.77
1616 2343 6.131544 AGAGCACGACAAGTTAAATTTTGT 57.868 33.333 0.00 0.00 40.04 2.83
1629 2356 2.309528 AACACTGAAAGAGCACGACA 57.690 45.000 0.00 0.00 37.43 4.35
1717 2444 4.771114 CCCCCATTGTACAGAATCAGTA 57.229 45.455 0.00 0.00 0.00 2.74
1868 2595 0.108585 TTGGCTCTGAGGGTGTTGAC 59.891 55.000 6.83 0.00 0.00 3.18
1964 2691 3.245622 TGGTCAATCTCTCACTACCAGGA 60.246 47.826 0.00 0.00 33.28 3.86
2377 3104 1.899814 TGTCAGGATACACACCCAGAC 59.100 52.381 0.00 0.00 41.41 3.51
2396 3123 1.291184 TGTTTCGCCACTGCTCGATG 61.291 55.000 0.00 0.00 34.48 3.84
2444 3171 2.192664 TTTCAACAAGCGGGCTCATA 57.807 45.000 0.00 0.00 0.00 2.15
2651 3378 3.198872 GAGATAAGCTAACTGGTGGTGC 58.801 50.000 0.00 0.00 0.00 5.01
2825 3552 2.834689 CGCAAGTTGATGGAAACGTAC 58.165 47.619 7.16 0.00 35.13 3.67
2916 3644 6.038714 GGTTTGGGCTGTATAGAGAAGAATTG 59.961 42.308 0.05 0.00 0.00 2.32
3079 3809 4.081917 TGAACAGTATAATCAGCACGGACA 60.082 41.667 0.00 0.00 0.00 4.02
3221 3951 7.625828 AGATATAAGTAAACAAGTTGCACCC 57.374 36.000 1.81 0.00 0.00 4.61
3360 4091 4.083590 GCAGCAAACAAGTAGAGAAGAAGG 60.084 45.833 0.00 0.00 0.00 3.46
3477 4208 1.610886 GGAAACCTCTCTTTCGGTGGG 60.611 57.143 0.00 0.00 32.86 4.61
3549 4280 0.674895 CCACAGCCAGTACAAGAGCC 60.675 60.000 0.00 0.00 0.00 4.70
3586 4317 7.775053 TCTTGTCCCAGTATAAAGCAAAAAT 57.225 32.000 0.00 0.00 0.00 1.82
3595 4326 5.235850 TGCAGTTTCTTGTCCCAGTATAA 57.764 39.130 0.00 0.00 0.00 0.98
3612 4343 4.464008 TCACCTGAAGAGAAAATTGCAGT 58.536 39.130 0.00 0.00 0.00 4.40
3639 4370 8.819974 CATGATTAATTGGTTAACAGAAATGCC 58.180 33.333 8.10 0.00 32.91 4.40
3681 4412 9.255304 GATTACATTTGACAGTTAAGGCAAAAA 57.745 29.630 0.00 0.00 34.38 1.94
3702 4433 7.739022 TTCGCAATTCATGTTCAATGATTAC 57.261 32.000 0.00 0.00 0.00 1.89
3723 4454 4.739046 ACTCTCTGTTTCAGCAATTTCG 57.261 40.909 0.00 0.00 0.00 3.46
3738 4469 8.798859 ATGTTGCATGTCTTATTAAACTCTCT 57.201 30.769 0.00 0.00 0.00 3.10
3756 4487 8.169977 AGAAAGATTAAACTCTCAATGTTGCA 57.830 30.769 0.00 0.00 0.00 4.08
3767 4498 5.357314 GGCAAGGGGTAGAAAGATTAAACTC 59.643 44.000 0.00 0.00 0.00 3.01
3772 4503 4.108570 TCAGGCAAGGGGTAGAAAGATTA 58.891 43.478 0.00 0.00 0.00 1.75
3780 4619 3.864789 ATACAATCAGGCAAGGGGTAG 57.135 47.619 0.00 0.00 0.00 3.18
3790 4629 6.083098 TGTTCACACCAAAATACAATCAGG 57.917 37.500 0.00 0.00 0.00 3.86
3794 4633 6.041409 TCACCATGTTCACACCAAAATACAAT 59.959 34.615 0.00 0.00 0.00 2.71
3795 4634 5.360999 TCACCATGTTCACACCAAAATACAA 59.639 36.000 0.00 0.00 0.00 2.41
3801 4640 3.956848 TGATTCACCATGTTCACACCAAA 59.043 39.130 0.00 0.00 0.00 3.28
3846 4686 3.684788 ACTACTCGGTGTCAAAATCATGC 59.315 43.478 0.00 0.00 0.00 4.06
3860 4700 1.191647 GCGTCACAACAAACTACTCGG 59.808 52.381 0.00 0.00 0.00 4.63
3861 4701 1.855978 TGCGTCACAACAAACTACTCG 59.144 47.619 0.00 0.00 0.00 4.18
3879 4719 8.519492 TGAAGCTCAACTTAAATTAAATGTGC 57.481 30.769 13.00 13.00 39.29 4.57
3929 4769 7.067372 TGCAACTATTGTCATGCTAAGCTAAAT 59.933 33.333 5.73 0.00 39.49 1.40
3974 4815 2.231964 CCTTGCCATGCATACAAACACT 59.768 45.455 13.53 0.00 38.76 3.55
4136 5044 6.741811 GTGAAAACACGTGTGTACAACATTAA 59.258 34.615 24.16 0.00 44.13 1.40
4159 5068 1.882623 GCTGTTCTTCCCTGGAAAGTG 59.117 52.381 0.00 0.00 33.34 3.16
4228 5137 2.994699 CCCCTGACAATACCGCCA 59.005 61.111 0.00 0.00 0.00 5.69
4347 5256 6.776116 TCTCCTTCAGTTCAGAGTAGTACAAA 59.224 38.462 2.52 0.00 0.00 2.83
4350 5259 8.508883 TTATCTCCTTCAGTTCAGAGTAGTAC 57.491 38.462 0.00 0.00 0.00 2.73
4351 5260 9.702253 ATTTATCTCCTTCAGTTCAGAGTAGTA 57.298 33.333 0.00 0.00 0.00 1.82
4352 5261 8.602472 ATTTATCTCCTTCAGTTCAGAGTAGT 57.398 34.615 0.00 0.00 0.00 2.73
4511 5422 5.924475 ACATTAAGGAGTTTGAACAGTCG 57.076 39.130 0.00 0.00 0.00 4.18
4700 5651 0.458716 GCCACAGAAGACGAGGTAGC 60.459 60.000 0.00 0.00 0.00 3.58
4769 5722 6.598064 GCAAACCCTAAAGAGACTAGCATAAA 59.402 38.462 0.00 0.00 0.00 1.40
4844 5819 1.267121 GTGAGGGCTAGGTGAGAACA 58.733 55.000 0.00 0.00 0.00 3.18
4863 5841 0.180171 TATGAGATGCACCGTTGGGG 59.820 55.000 0.00 0.00 43.62 4.96
4885 5863 2.920912 TCCACACACCCTCCGGAC 60.921 66.667 0.00 0.00 0.00 4.79
4886 5864 2.603473 CTCCACACACCCTCCGGA 60.603 66.667 2.93 2.93 0.00 5.14
4895 5873 1.046472 ACCGAAGACACCTCCACACA 61.046 55.000 0.00 0.00 0.00 3.72
4924 5905 0.110486 ACAAGCACGGACCAAATCCT 59.890 50.000 0.00 0.00 46.69 3.24
4935 5916 1.732259 GACCCAACATAGACAAGCACG 59.268 52.381 0.00 0.00 0.00 5.34
4946 5927 0.392998 GATCCACGCAGACCCAACAT 60.393 55.000 0.00 0.00 0.00 2.71
4990 5972 6.806751 TCGAAAGAATCTAACCTATGGACAG 58.193 40.000 0.00 0.00 37.03 3.51
5279 7244 9.591792 CATCTAGATGTGAATTAGACAAACTGA 57.408 33.333 22.42 0.00 34.23 3.41


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

AutoCloner maintained by Alex Coulton.