Multiple sequence alignment - TraesCS5D01G430500

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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 TraesCS5D01G430500 chr5D 100.000 6102 0 0 1 6102 487884694 487878593 0.000000e+00 11269.0
1 TraesCS5D01G430500 chr5D 85.714 203 18 4 2076 2269 487882437 487882237 2.880000e-48 204.0
2 TraesCS5D01G430500 chr5D 85.714 203 18 4 2258 2458 487882619 487882426 2.880000e-48 204.0
3 TraesCS5D01G430500 chr5D 91.549 71 5 1 6032 6102 121341049 121340980 5.030000e-16 97.1
4 TraesCS5D01G430500 chr5D 96.552 58 2 0 5152 5209 487879485 487879428 5.030000e-16 97.1
5 TraesCS5D01G430500 chr5D 97.368 38 1 0 3285 3322 421997896 421997859 1.420000e-06 65.8
6 TraesCS5D01G430500 chr5B 93.281 3944 170 38 449 4349 600492450 600488559 0.000000e+00 5727.0
7 TraesCS5D01G430500 chr5B 91.434 2218 101 32 1 2180 600492869 600490703 0.000000e+00 2961.0
8 TraesCS5D01G430500 chr5B 90.557 826 44 9 4351 5171 600488477 600487681 0.000000e+00 1062.0
9 TraesCS5D01G430500 chr5B 86.528 193 17 2 2076 2260 600490653 600490462 2.880000e-48 204.0
10 TraesCS5D01G430500 chr5A 91.053 3979 247 57 1 3917 608608502 608604571 0.000000e+00 5275.0
11 TraesCS5D01G430500 chr5A 89.486 1322 95 24 3857 5171 608604577 608603293 0.000000e+00 1631.0
12 TraesCS5D01G430500 chr5A 89.855 69 6 1 6028 6095 665889355 665889423 3.030000e-13 87.9
13 TraesCS5D01G430500 chr5A 92.683 41 3 0 3284 3324 565495083 565495043 6.610000e-05 60.2
14 TraesCS5D01G430500 chr3D 87.931 812 78 11 5236 6032 517294425 517293619 0.000000e+00 939.0
15 TraesCS5D01G430500 chr3D 89.079 467 41 4 5576 6032 549353014 549352548 6.860000e-159 571.0
16 TraesCS5D01G430500 chr2D 86.675 803 93 7 5240 6032 555476392 555477190 0.000000e+00 878.0
17 TraesCS5D01G430500 chr2D 86.275 816 89 11 5236 6032 424176412 424177223 0.000000e+00 865.0
18 TraesCS5D01G430500 chr2D 81.636 550 91 7 5267 5811 400510558 400510014 1.210000e-121 448.0
19 TraesCS5D01G430500 chr2D 86.250 80 10 1 6024 6102 168422989 168423068 1.090000e-12 86.1
20 TraesCS5D01G430500 chr2D 83.529 85 8 2 3283 3361 74975909 74975993 2.360000e-09 75.0
21 TraesCS5D01G430500 chr2A 86.101 813 93 8 5236 6032 757681735 757682543 0.000000e+00 857.0
22 TraesCS5D01G430500 chr2A 92.958 71 4 1 6032 6102 526100898 526100829 1.080000e-17 102.0
23 TraesCS5D01G430500 chr1B 85.910 802 79 16 5238 6032 159638658 159639432 0.000000e+00 824.0
24 TraesCS5D01G430500 chr1B 86.872 716 85 5 5236 5944 65290292 65291005 0.000000e+00 793.0
25 TraesCS5D01G430500 chr1B 85.133 565 73 6 5236 5793 121235693 121236253 8.880000e-158 568.0
26 TraesCS5D01G430500 chr1B 88.750 80 7 2 6024 6102 67505004 67505082 5.030000e-16 97.1
27 TraesCS5D01G430500 chr1B 93.846 65 3 1 6028 6091 253011148 253011212 5.030000e-16 97.1
28 TraesCS5D01G430500 chr1B 90.909 44 2 2 3425 3466 229255911 229255954 2.380000e-04 58.4
29 TraesCS5D01G430500 chr4B 83.210 810 117 12 5236 6032 614127612 614126809 0.000000e+00 725.0
30 TraesCS5D01G430500 chr4B 86.420 81 9 2 3281 3361 370424038 370424116 3.030000e-13 87.9
31 TraesCS5D01G430500 chr4B 88.333 60 4 3 3280 3338 606917385 606917328 1.100000e-07 69.4
32 TraesCS5D01G430500 chr6D 84.172 676 89 11 5374 6040 437934633 437933967 1.850000e-179 640.0
33 TraesCS5D01G430500 chr6D 88.462 52 5 1 5164 5215 437934731 437934681 1.840000e-05 62.1
34 TraesCS5D01G430500 chr7A 91.250 80 6 1 6024 6102 641726774 641726695 2.330000e-19 108.0
35 TraesCS5D01G430500 chr4D 90.141 71 6 1 6032 6102 439740819 439740888 2.340000e-14 91.6
36 TraesCS5D01G430500 chr2B 88.158 76 7 2 6028 6102 8283023 8282949 8.420000e-14 89.8
37 TraesCS5D01G430500 chr6A 100.000 31 0 0 5178 5208 109492137 109492107 2.380000e-04 58.4
38 TraesCS5D01G430500 chr1D 90.909 44 2 2 3425 3466 128523552 128523595 2.380000e-04 58.4
39 TraesCS5D01G430500 chr1A 90.909 44 2 2 3425 3466 188144000 188144043 2.380000e-04 58.4


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 TraesCS5D01G430500 chr5D 487878593 487884694 6101 True 11269.00 11269 100.0000 1 6102 1 chr5D.!!$R3 6101
1 TraesCS5D01G430500 chr5B 600487681 600492869 5188 True 2488.50 5727 90.4500 1 5171 4 chr5B.!!$R1 5170
2 TraesCS5D01G430500 chr5A 608603293 608608502 5209 True 3453.00 5275 90.2695 1 5171 2 chr5A.!!$R2 5170
3 TraesCS5D01G430500 chr3D 517293619 517294425 806 True 939.00 939 87.9310 5236 6032 1 chr3D.!!$R1 796
4 TraesCS5D01G430500 chr2D 555476392 555477190 798 False 878.00 878 86.6750 5240 6032 1 chr2D.!!$F4 792
5 TraesCS5D01G430500 chr2D 424176412 424177223 811 False 865.00 865 86.2750 5236 6032 1 chr2D.!!$F3 796
6 TraesCS5D01G430500 chr2D 400510014 400510558 544 True 448.00 448 81.6360 5267 5811 1 chr2D.!!$R1 544
7 TraesCS5D01G430500 chr2A 757681735 757682543 808 False 857.00 857 86.1010 5236 6032 1 chr2A.!!$F1 796
8 TraesCS5D01G430500 chr1B 159638658 159639432 774 False 824.00 824 85.9100 5238 6032 1 chr1B.!!$F4 794
9 TraesCS5D01G430500 chr1B 65290292 65291005 713 False 793.00 793 86.8720 5236 5944 1 chr1B.!!$F1 708
10 TraesCS5D01G430500 chr1B 121235693 121236253 560 False 568.00 568 85.1330 5236 5793 1 chr1B.!!$F3 557
11 TraesCS5D01G430500 chr4B 614126809 614127612 803 True 725.00 725 83.2100 5236 6032 1 chr4B.!!$R2 796
12 TraesCS5D01G430500 chr6D 437933967 437934731 764 True 351.05 640 86.3170 5164 6040 2 chr6D.!!$R1 876

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
60 61 0.955428 GCCCAAGAATCGTCACTGCA 60.955 55.000 0.00 0.00 0.00 4.41 F
258 262 1.664321 CTCCCCATCTTTGCAGCTGC 61.664 60.000 31.89 31.89 42.50 5.25 F
1339 1393 0.253044 TTGGCTTATCCGAGCAAGCT 59.747 50.000 14.12 0.00 45.20 3.74 F
1865 1927 0.592637 CTCACGCAAATGCTGTTCCA 59.407 50.000 3.63 0.00 39.32 3.53 F
3032 3135 2.017049 CTAAGCAGTGTATTGGGTGGC 58.983 52.381 0.00 0.00 0.00 5.01 F
3292 3395 2.993899 GTGTTGTCAATGTACTCCCTCG 59.006 50.000 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1114 0.609681 GGCGGATCTAGGACGAGGAT 60.610 60.000 0.00 0.00 0.00 3.24 R
1884 1946 1.136336 GTTTTACAAGCTGAGTCGGCG 60.136 52.381 18.16 0.00 41.21 6.46 R
2735 2838 2.301577 TTCCCTGCAAAACAAAACCG 57.698 45.000 0.00 0.00 0.00 4.44 R
3420 3538 1.447314 GGCCCCGACAGTAAACTCG 60.447 63.158 0.00 0.00 0.00 4.18 R
4052 4226 0.100682 CAATCATGTGCTGCAGAGCC 59.899 55.000 20.43 4.19 45.57 4.70 R
5234 5494 0.035915 TATGCAGCCTACCAAACGCA 60.036 50.000 0.00 0.00 0.00 5.24 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
39 40 5.506832 CGCGAAAAGTGTAACCATAACAATC 59.493 40.000 0.00 0.00 37.80 2.67
45 46 4.013728 GTGTAACCATAACAATCAGCCCA 58.986 43.478 0.00 0.00 0.00 5.36
60 61 0.955428 GCCCAAGAATCGTCACTGCA 60.955 55.000 0.00 0.00 0.00 4.41
78 82 3.142174 TGCAAACATACCAACGATGACA 58.858 40.909 0.00 0.00 0.00 3.58
149 153 2.341257 ACAGTTCACGAAGCAGCATAG 58.659 47.619 0.00 0.00 0.00 2.23
193 197 3.898123 AGTAAGTCTTCTTCAGCAGGTGA 59.102 43.478 0.00 0.00 35.36 4.02
258 262 1.664321 CTCCCCATCTTTGCAGCTGC 61.664 60.000 31.89 31.89 42.50 5.25
267 271 2.957484 TTTGCAGCTGCGGCACAAAG 62.957 55.000 32.11 10.88 45.83 2.77
269 273 2.979676 CAGCTGCGGCACAAAGGA 60.980 61.111 21.93 0.00 41.70 3.36
328 332 4.499183 CACAAAATCTAGCGGAAGACTCT 58.501 43.478 0.00 0.00 0.00 3.24
378 382 2.688958 GCGCTCCTAGTCCTAAGAAGAA 59.311 50.000 0.00 0.00 0.00 2.52
542 546 2.058595 CCCAGATCGGACGGAAGGT 61.059 63.158 5.32 0.00 36.56 3.50
629 645 2.415010 CGGTGGCTCTGGATCTCG 59.585 66.667 0.00 0.00 0.00 4.04
1069 1114 0.689623 TTTTACCCCCGGCGACTTTA 59.310 50.000 9.30 0.00 0.00 1.85
1133 1185 5.912892 TCTCGCTGTAATTGTGATTGGATA 58.087 37.500 0.00 0.00 0.00 2.59
1292 1344 4.096003 GCGTAAGAGCCCAGCCCA 62.096 66.667 0.00 0.00 43.02 5.36
1322 1375 1.078709 ATCGTCTGCGTCACCATTTG 58.921 50.000 0.00 0.00 39.49 2.32
1327 1381 1.164411 CTGCGTCACCATTTGGCTTA 58.836 50.000 0.00 0.00 39.32 3.09
1329 1383 1.742831 TGCGTCACCATTTGGCTTATC 59.257 47.619 0.00 0.00 39.32 1.75
1332 1386 2.639065 GTCACCATTTGGCTTATCCGA 58.361 47.619 0.00 0.00 39.32 4.55
1339 1393 0.253044 TTGGCTTATCCGAGCAAGCT 59.747 50.000 14.12 0.00 45.20 3.74
1455 1515 4.651962 TGATGATCAATGATGCATGGGTTT 59.348 37.500 2.46 0.00 0.00 3.27
1550 1611 1.247419 ATCGGCCAAATCGGTTGCAA 61.247 50.000 2.24 0.00 35.74 4.08
1589 1650 7.278868 GGAGACATGGAGTTAGTTCACTTTATG 59.721 40.741 0.00 0.00 31.61 1.90
1705 1767 2.860293 CGCTGTGTGGCCTTAACG 59.140 61.111 3.32 0.00 0.00 3.18
1768 1830 1.729586 TTCTACACAAGACCAGGGCT 58.270 50.000 0.00 0.00 32.51 5.19
1774 1836 1.078426 CAAGACCAGGGCTTACCGG 60.078 63.158 7.45 0.00 46.96 5.28
1811 1873 2.089980 AGCTGCACATTGGTTCATCTC 58.910 47.619 1.02 0.00 0.00 2.75
1822 1884 4.437682 TGGTTCATCTCTTGACAAGGTT 57.562 40.909 15.13 0.00 32.84 3.50
1855 1917 1.106351 ACCATGCAACCTCACGCAAA 61.106 50.000 0.00 0.00 42.37 3.68
1865 1927 0.592637 CTCACGCAAATGCTGTTCCA 59.407 50.000 3.63 0.00 39.32 3.53
1884 1946 4.466827 TCCACCTTTTCAAACTCCCTAAC 58.533 43.478 0.00 0.00 0.00 2.34
2018 2088 6.889177 TGCTACCATGATCATTGGAGTTAAAA 59.111 34.615 23.03 4.60 0.00 1.52
2144 2214 7.145323 TCTACTTTTATTCAAGCAACAAAGGC 58.855 34.615 0.00 0.00 0.00 4.35
2175 2245 9.826574 AACAATTAGCAATTTAGCATCATCAAT 57.173 25.926 0.00 0.00 36.85 2.57
2182 2252 8.139989 AGCAATTTAGCATCATCAATACTTTCC 58.860 33.333 0.00 0.00 36.85 3.13
2183 2253 8.139989 GCAATTTAGCATCATCAATACTTTCCT 58.860 33.333 0.00 0.00 0.00 3.36
2187 2257 9.905713 TTTAGCATCATCAATACTTTCCTAGTT 57.094 29.630 0.00 0.00 38.33 2.24
2188 2258 9.905713 TTAGCATCATCAATACTTTCCTAGTTT 57.094 29.630 0.00 0.00 38.33 2.66
2189 2259 8.814038 AGCATCATCAATACTTTCCTAGTTTT 57.186 30.769 0.00 0.00 38.33 2.43
2190 2260 9.905713 AGCATCATCAATACTTTCCTAGTTTTA 57.094 29.630 0.00 0.00 38.33 1.52
2191 2261 9.937175 GCATCATCAATACTTTCCTAGTTTTAC 57.063 33.333 0.00 0.00 38.33 2.01
2388 2489 8.713737 ATACTTTCCTAGTTTCACGATTTACC 57.286 34.615 0.00 0.00 38.33 2.85
2451 2552 3.921104 TCATCTGTCCTAGATCTGCCTT 58.079 45.455 5.18 0.00 44.34 4.35
2474 2575 8.928733 CCTTCCATTTTTCTTGTTCATATTGTG 58.071 33.333 0.00 0.00 0.00 3.33
2498 2599 5.453903 GCCTGTATCATATGACACCTTCAGT 60.454 44.000 11.52 0.00 37.77 3.41
2626 2727 7.392953 TGGCACTCATGTTGTAATATTTTCTGA 59.607 33.333 0.00 0.00 0.00 3.27
2735 2838 2.113860 TCTCTTATGTGCCTGGTTGC 57.886 50.000 0.00 0.00 0.00 4.17
3031 3134 2.026262 ACCTAAGCAGTGTATTGGGTGG 60.026 50.000 14.53 5.31 38.67 4.61
3032 3135 2.017049 CTAAGCAGTGTATTGGGTGGC 58.983 52.381 0.00 0.00 0.00 5.01
3151 3254 5.539582 TTGACATTACAAGGTATCGTTGC 57.460 39.130 2.76 0.00 33.25 4.17
3173 3276 7.887996 TGCATGCTTGTATCCTTTTTAAAAG 57.112 32.000 20.33 10.23 0.00 2.27
3292 3395 2.993899 GTGTTGTCAATGTACTCCCTCG 59.006 50.000 0.00 0.00 0.00 4.63
3309 3412 8.175925 ACTCCCTCGGTACTAAAATATAAGAC 57.824 38.462 0.00 0.00 0.00 3.01
3629 3747 8.459911 TGGTATAGAAGAATCTTATGTCGACA 57.540 34.615 22.48 22.48 37.10 4.35
3643 3761 4.747540 TGTCGACAATTTCCTGTGAATG 57.252 40.909 17.62 0.00 0.00 2.67
3727 3845 7.880059 TCATCTGCTATATTCATTGTCGAAG 57.120 36.000 0.00 0.00 0.00 3.79
3824 3945 8.265764 ACCCTTCTATGTGTATTTTCTTAGTCC 58.734 37.037 0.00 0.00 0.00 3.85
3846 3967 7.345914 AGTCCTCATAATTTCTAGCTGTTAGGT 59.654 37.037 0.00 0.00 0.00 3.08
4052 4226 1.222936 GACCAGACAGATGCCCCAG 59.777 63.158 0.00 0.00 0.00 4.45
4112 4287 8.681486 TCATTGTATCCTACAGAATTGATTGG 57.319 34.615 0.00 0.00 40.24 3.16
4197 4372 2.283298 CAGAGCGCCTGTCAATACATT 58.717 47.619 15.27 0.00 38.10 2.71
4198 4373 2.286294 CAGAGCGCCTGTCAATACATTC 59.714 50.000 15.27 0.00 38.10 2.67
4201 4376 1.599542 GCGCCTGTCAATACATTCCTC 59.400 52.381 0.00 0.00 34.37 3.71
4210 4385 6.697395 TGTCAATACATTCCTCGGTATATGG 58.303 40.000 0.00 0.00 30.37 2.74
4213 4388 2.334977 ACATTCCTCGGTATATGGGCA 58.665 47.619 0.00 0.00 0.00 5.36
4215 4390 0.677288 TTCCTCGGTATATGGGCACG 59.323 55.000 0.00 0.00 0.00 5.34
4223 4398 0.544223 TATATGGGCACGCAGGTGTT 59.456 50.000 0.00 0.00 46.13 3.32
4227 4402 2.033194 GGGCACGCAGGTGTTCTAC 61.033 63.158 0.00 0.00 46.13 2.59
4230 4405 0.721718 GCACGCAGGTGTTCTACATC 59.278 55.000 0.00 0.00 46.13 3.06
4263 4438 4.884164 GCCCTAGCTTTCAATACTGAATGT 59.116 41.667 0.00 0.00 41.22 2.71
4265 4440 5.882557 CCCTAGCTTTCAATACTGAATGTGT 59.117 40.000 0.00 0.00 41.22 3.72
4284 4459 0.446616 TCGAGAGACGACGGATTGTG 59.553 55.000 0.00 0.00 46.45 3.33
4315 4490 8.250143 ACTGAAACTGGTTAATTTCCTTTCAT 57.750 30.769 12.54 5.88 34.52 2.57
4329 4504 9.533253 AATTTCCTTTCATTGTTTGTAGTTGAG 57.467 29.630 0.00 0.00 0.00 3.02
4349 4524 4.133078 GAGATTTCTTCCCATGCCTACTG 58.867 47.826 0.00 0.00 0.00 2.74
4355 4610 6.569127 TTCTTCCCATGCCTACTGTATAAA 57.431 37.500 0.00 0.00 0.00 1.40
4375 4630 0.841289 ACTGAAAAGGACCCGAACCA 59.159 50.000 0.00 0.00 0.00 3.67
4379 4634 2.304092 GAAAAGGACCCGAACCAACTT 58.696 47.619 0.00 0.00 0.00 2.66
4416 4672 1.610522 ACAATGCTGTGAAACCTGAGC 59.389 47.619 0.00 0.00 33.30 4.26
4417 4673 1.610038 CAATGCTGTGAAACCTGAGCA 59.390 47.619 0.00 0.00 45.12 4.26
4421 4677 1.457346 CTGTGAAACCTGAGCATCCC 58.543 55.000 0.00 0.00 34.36 3.85
4422 4678 1.004044 CTGTGAAACCTGAGCATCCCT 59.996 52.381 0.00 0.00 34.36 4.20
4560 4817 0.250684 TTCATCAAGACTTGCCGCCA 60.251 50.000 10.50 0.00 0.00 5.69
4667 4924 1.258982 CGCAGCGGATGTACTCATTTC 59.741 52.381 7.00 0.00 34.06 2.17
4668 4925 2.555199 GCAGCGGATGTACTCATTTCT 58.445 47.619 0.00 0.00 34.06 2.52
4765 5022 1.079256 TCCTGCTGGCCTCTGTACT 59.921 57.895 3.32 0.00 0.00 2.73
4769 5026 0.251787 TGCTGGCCTCTGTACTGAGA 60.252 55.000 26.29 9.70 36.23 3.27
4773 5030 1.139947 GCCTCTGTACTGAGACGCC 59.860 63.158 26.29 11.04 36.23 5.68
4774 5031 1.595993 GCCTCTGTACTGAGACGCCA 61.596 60.000 26.29 0.00 36.23 5.69
4805 5062 1.712977 ATCGTCTCCGGTGAGCGTAC 61.713 60.000 20.07 5.62 38.45 3.67
4811 5068 4.111016 CGGTGAGCGTACGCCTGA 62.111 66.667 34.88 17.38 43.17 3.86
4897 5157 2.772515 AGGAGTAGGTATTTGCCCTGTC 59.227 50.000 0.00 0.00 33.35 3.51
4944 5204 1.268283 ACAGGGCCTCTCTACCTTGC 61.268 60.000 0.95 0.00 36.54 4.01
4988 5248 3.403038 ACTCCAGTGTCTGTATGTTTGC 58.597 45.455 0.00 0.00 0.00 3.68
5141 5401 3.495629 GGTTTCCACGGGTTACTTTCTCT 60.496 47.826 0.00 0.00 0.00 3.10
5150 5410 4.393062 CGGGTTACTTTCTCTACTGACGTA 59.607 45.833 0.00 0.00 0.00 3.57
5155 5415 4.734917 ACTTTCTCTACTGACGTATGTGC 58.265 43.478 0.00 0.00 0.00 4.57
5171 5431 2.679450 TGTGCGTTCGTATAGTTGCTT 58.321 42.857 0.00 0.00 0.00 3.91
5172 5432 3.835779 TGTGCGTTCGTATAGTTGCTTA 58.164 40.909 0.00 0.00 0.00 3.09
5173 5433 3.609373 TGTGCGTTCGTATAGTTGCTTAC 59.391 43.478 0.00 0.00 0.00 2.34
5174 5434 2.847717 TGCGTTCGTATAGTTGCTTACG 59.152 45.455 0.00 0.00 41.85 3.18
5175 5435 2.214914 GCGTTCGTATAGTTGCTTACGG 59.785 50.000 0.00 0.00 41.08 4.02
5209 5469 0.625316 TGCATACAGCCCAATCAGGT 59.375 50.000 0.00 0.00 44.83 4.00
5210 5470 1.027357 GCATACAGCCCAATCAGGTG 58.973 55.000 0.00 0.00 38.67 4.00
5211 5471 1.683011 GCATACAGCCCAATCAGGTGT 60.683 52.381 1.00 1.00 46.86 4.16
5212 5472 2.019249 CATACAGCCCAATCAGGTGTG 58.981 52.381 5.90 0.00 45.05 3.82
5213 5473 0.322456 TACAGCCCAATCAGGTGTGC 60.322 55.000 5.90 0.00 45.05 4.57
5214 5474 2.360350 AGCCCAATCAGGTGTGCG 60.360 61.111 0.00 0.00 34.66 5.34
5215 5475 2.672996 GCCCAATCAGGTGTGCGT 60.673 61.111 0.00 0.00 34.66 5.24
5216 5476 2.268076 GCCCAATCAGGTGTGCGTT 61.268 57.895 0.00 0.00 34.66 4.84
5217 5477 1.875963 CCCAATCAGGTGTGCGTTC 59.124 57.895 0.00 0.00 34.66 3.95
5218 5478 1.497278 CCAATCAGGTGTGCGTTCG 59.503 57.895 0.00 0.00 0.00 3.95
5219 5479 1.227999 CCAATCAGGTGTGCGTTCGT 61.228 55.000 0.00 0.00 0.00 3.85
5220 5480 1.424403 CAATCAGGTGTGCGTTCGTA 58.576 50.000 0.00 0.00 0.00 3.43
5221 5481 1.999735 CAATCAGGTGTGCGTTCGTAT 59.000 47.619 0.00 0.00 0.00 3.06
5222 5482 3.183754 CAATCAGGTGTGCGTTCGTATA 58.816 45.455 0.00 0.00 0.00 1.47
5223 5483 2.554806 TCAGGTGTGCGTTCGTATAG 57.445 50.000 0.00 0.00 0.00 1.31
5224 5484 1.814394 TCAGGTGTGCGTTCGTATAGT 59.186 47.619 0.00 0.00 0.00 2.12
5225 5485 2.159476 TCAGGTGTGCGTTCGTATAGTC 60.159 50.000 0.00 0.00 0.00 2.59
5226 5486 1.186030 GGTGTGCGTTCGTATAGTCG 58.814 55.000 0.00 0.00 0.00 4.18
5232 5492 1.700404 GCGTTCGTATAGTCGCTTACG 59.300 52.381 0.00 0.00 44.28 3.18
5233 5493 2.293100 CGTTCGTATAGTCGCTTACGG 58.707 52.381 14.55 0.00 41.08 4.02
5234 5494 2.285834 CGTTCGTATAGTCGCTTACGGT 60.286 50.000 14.55 0.00 41.08 4.83
5267 5527 2.775890 CTGCATACAGCCTAATCAGGG 58.224 52.381 0.00 0.00 44.83 4.45
5347 5607 0.037734 CGGACCTTAAAGCACCCCTT 59.962 55.000 0.00 0.00 34.51 3.95
5360 5620 2.356278 CCCTTAGCCTGGCTTGCA 59.644 61.111 28.55 5.93 40.44 4.08
5366 5626 1.788518 TAGCCTGGCTTGCAGGGAAA 61.789 55.000 28.55 1.54 40.44 3.13
5408 5668 3.640407 GCCAGACTGAGTGGGGCA 61.640 66.667 16.60 0.00 44.01 5.36
5429 5689 1.326548 GAAAACGAAGACGCGGCATAT 59.673 47.619 17.71 0.00 43.96 1.78
5516 5778 2.512056 CCAAATATACCCTCACCACCCA 59.488 50.000 0.00 0.00 0.00 4.51
5528 5790 2.176798 TCACCACCCAATTTCCTCACTT 59.823 45.455 0.00 0.00 0.00 3.16
5529 5791 2.297033 CACCACCCAATTTCCTCACTTG 59.703 50.000 0.00 0.00 0.00 3.16
5564 5828 3.547746 GACAAACCCTCTGTTGTTGGTA 58.452 45.455 0.00 0.00 37.23 3.25
5565 5829 3.284617 ACAAACCCTCTGTTGTTGGTAC 58.715 45.455 0.00 0.00 37.23 3.34
5568 5832 0.321298 CCCTCTGTTGTTGGTACCGG 60.321 60.000 7.57 0.00 0.00 5.28
5632 5899 1.078848 ACTGAGATCTGCGGTTGCC 60.079 57.895 0.00 0.00 41.78 4.52
5646 5913 3.067084 TTGCCACACTCCCCTGCAA 62.067 57.895 0.00 0.00 39.42 4.08
5743 6014 2.710902 CGTCTCCGCCATGTCTCCA 61.711 63.158 0.00 0.00 0.00 3.86
5744 6015 1.596934 GTCTCCGCCATGTCTCCAA 59.403 57.895 0.00 0.00 0.00 3.53
5824 6112 2.034305 CGATAGGAGTGTTTAGGGTCGG 59.966 54.545 0.00 0.00 0.00 4.79
5875 6163 4.081365 TGTCGCTTAGGTTGTGGATGAATA 60.081 41.667 0.00 0.00 0.00 1.75
5980 6272 1.022735 GAGAGACCTCGCATCCGTAA 58.977 55.000 0.00 0.00 35.54 3.18
6033 6325 5.861251 GGATAGCGAATCTGAACTACATCAG 59.139 44.000 0.00 0.00 46.62 2.90
6042 6334 4.558226 TGAACTACATCAGATGCTGGTT 57.442 40.909 10.59 12.03 31.51 3.67
6043 6335 4.910195 TGAACTACATCAGATGCTGGTTT 58.090 39.130 10.59 0.00 31.51 3.27
6044 6336 5.316167 TGAACTACATCAGATGCTGGTTTT 58.684 37.500 10.59 0.00 31.51 2.43
6045 6337 5.769662 TGAACTACATCAGATGCTGGTTTTT 59.230 36.000 10.59 0.00 31.51 1.94
6046 6338 5.633830 ACTACATCAGATGCTGGTTTTTG 57.366 39.130 10.59 0.00 31.51 2.44
6047 6339 3.947910 ACATCAGATGCTGGTTTTTGG 57.052 42.857 10.59 0.00 31.51 3.28
6048 6340 2.028748 ACATCAGATGCTGGTTTTTGGC 60.029 45.455 10.59 0.00 31.51 4.52
6049 6341 0.968405 TCAGATGCTGGTTTTTGGCC 59.032 50.000 0.00 0.00 31.51 5.36
6050 6342 0.971386 CAGATGCTGGTTTTTGGCCT 59.029 50.000 3.32 0.00 0.00 5.19
6051 6343 0.971386 AGATGCTGGTTTTTGGCCTG 59.029 50.000 3.32 0.00 0.00 4.85
6052 6344 0.671472 GATGCTGGTTTTTGGCCTGC 60.671 55.000 3.32 6.31 46.73 4.85
6053 6345 2.820973 GCTGGTTTTTGGCCTGCA 59.179 55.556 3.32 0.00 46.11 4.41
6054 6346 1.372307 GCTGGTTTTTGGCCTGCAT 59.628 52.632 3.32 0.00 46.11 3.96
6055 6347 0.250424 GCTGGTTTTTGGCCTGCATT 60.250 50.000 3.32 0.00 46.11 3.56
6056 6348 1.815021 GCTGGTTTTTGGCCTGCATTT 60.815 47.619 3.32 0.00 46.11 2.32
6057 6349 1.874872 CTGGTTTTTGGCCTGCATTTG 59.125 47.619 3.32 0.00 0.00 2.32
6058 6350 0.592637 GGTTTTTGGCCTGCATTTGC 59.407 50.000 3.32 0.00 42.50 3.68
6059 6351 1.596603 GTTTTTGGCCTGCATTTGCT 58.403 45.000 3.32 0.00 42.66 3.91
6060 6352 1.532437 GTTTTTGGCCTGCATTTGCTC 59.468 47.619 3.32 0.00 42.66 4.26
6061 6353 0.757512 TTTTGGCCTGCATTTGCTCA 59.242 45.000 3.32 0.00 42.66 4.26
6062 6354 0.757512 TTTGGCCTGCATTTGCTCAA 59.242 45.000 3.32 1.57 42.66 3.02
6063 6355 0.033781 TTGGCCTGCATTTGCTCAAC 59.966 50.000 3.32 0.00 42.66 3.18
6064 6356 1.079612 GGCCTGCATTTGCTCAACC 60.080 57.895 0.00 0.00 42.66 3.77
6065 6357 1.667151 GCCTGCATTTGCTCAACCA 59.333 52.632 3.94 0.00 42.66 3.67
6066 6358 0.389426 GCCTGCATTTGCTCAACCAG 60.389 55.000 3.94 0.00 42.66 4.00
6067 6359 0.245539 CCTGCATTTGCTCAACCAGG 59.754 55.000 3.94 8.02 42.66 4.45
6068 6360 0.389426 CTGCATTTGCTCAACCAGGC 60.389 55.000 3.94 0.00 42.66 4.85
6069 6361 1.079612 GCATTTGCTCAACCAGGCC 60.080 57.895 0.00 0.00 38.21 5.19
6070 6362 1.593265 CATTTGCTCAACCAGGCCC 59.407 57.895 0.00 0.00 0.00 5.80
6071 6363 1.155859 ATTTGCTCAACCAGGCCCA 59.844 52.632 0.00 0.00 0.00 5.36
6072 6364 0.471591 ATTTGCTCAACCAGGCCCAA 60.472 50.000 0.00 0.00 0.00 4.12
6073 6365 1.398958 TTTGCTCAACCAGGCCCAAC 61.399 55.000 0.00 0.00 0.00 3.77
6074 6366 2.116125 GCTCAACCAGGCCCAACT 59.884 61.111 0.00 0.00 0.00 3.16
6075 6367 2.270986 GCTCAACCAGGCCCAACTG 61.271 63.158 0.00 0.00 38.21 3.16
6076 6368 1.455849 CTCAACCAGGCCCAACTGA 59.544 57.895 0.00 0.00 40.97 3.41
6077 6369 0.607489 CTCAACCAGGCCCAACTGAG 60.607 60.000 0.00 3.40 40.97 3.35
6078 6370 1.059584 TCAACCAGGCCCAACTGAGA 61.060 55.000 0.00 0.00 40.97 3.27
6079 6371 0.890996 CAACCAGGCCCAACTGAGAC 60.891 60.000 0.00 0.00 40.97 3.36
6080 6372 1.352622 AACCAGGCCCAACTGAGACA 61.353 55.000 0.00 0.00 40.97 3.41
6081 6373 1.352622 ACCAGGCCCAACTGAGACAA 61.353 55.000 0.00 0.00 40.97 3.18
6082 6374 0.607489 CCAGGCCCAACTGAGACAAG 60.607 60.000 0.00 0.00 40.97 3.16
6083 6375 0.109342 CAGGCCCAACTGAGACAAGT 59.891 55.000 0.00 0.00 40.97 3.16
6084 6376 1.347707 CAGGCCCAACTGAGACAAGTA 59.652 52.381 0.00 0.00 40.97 2.24
6085 6377 2.026822 CAGGCCCAACTGAGACAAGTAT 60.027 50.000 0.00 0.00 40.97 2.12
6086 6378 2.026822 AGGCCCAACTGAGACAAGTATG 60.027 50.000 0.00 0.00 0.00 2.39
6087 6379 1.740025 GCCCAACTGAGACAAGTATGC 59.260 52.381 0.00 0.00 0.00 3.14
6088 6380 2.875672 GCCCAACTGAGACAAGTATGCA 60.876 50.000 0.00 0.00 0.00 3.96
6089 6381 3.411446 CCCAACTGAGACAAGTATGCAA 58.589 45.455 0.00 0.00 0.00 4.08
6090 6382 3.820467 CCCAACTGAGACAAGTATGCAAA 59.180 43.478 0.00 0.00 0.00 3.68
6091 6383 4.278170 CCCAACTGAGACAAGTATGCAAAA 59.722 41.667 0.00 0.00 0.00 2.44
6092 6384 5.047802 CCCAACTGAGACAAGTATGCAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
6093 6385 5.860182 CCAACTGAGACAAGTATGCAAAATG 59.140 40.000 0.00 0.00 0.00 2.32
6094 6386 5.051891 ACTGAGACAAGTATGCAAAATGC 57.948 39.130 0.00 0.00 45.29 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.081892 CAGTGACGATTCTTGGGCTG 58.918 55.000 0.00 0.00 0.00 4.85
45 46 4.154195 GGTATGTTTGCAGTGACGATTCTT 59.846 41.667 0.00 0.00 0.00 2.52
60 61 3.655486 TCGTGTCATCGTTGGTATGTTT 58.345 40.909 0.00 0.00 0.00 2.83
149 153 4.330250 TCGGGTGCTATAGGTACATAGAC 58.670 47.826 1.04 1.46 31.24 2.59
193 197 4.077184 TTCCCGCACGCCGAAGAT 62.077 61.111 0.00 0.00 40.02 2.40
258 262 1.201414 GGTTGGTATTCCTTTGTGCCG 59.799 52.381 0.00 0.00 34.23 5.69
267 271 3.676324 CGTCTGACTGAGGTTGGTATTCC 60.676 52.174 6.21 0.00 0.00 3.01
269 273 2.353803 GCGTCTGACTGAGGTTGGTATT 60.354 50.000 6.21 0.00 33.47 1.89
328 332 5.630415 ATGGAGAATTCCCGTCAAATCTA 57.370 39.130 0.65 0.00 43.33 1.98
378 382 3.266510 TGCATACTTGAAGAATCGCCT 57.733 42.857 0.00 0.00 0.00 5.52
392 396 0.443869 CGTGCTGGTCTGTTGCATAC 59.556 55.000 0.00 0.00 39.00 2.39
396 400 0.593128 ATTTCGTGCTGGTCTGTTGC 59.407 50.000 0.00 0.00 0.00 4.17
464 468 3.775654 CCTCTTCCCCTCGCGCTT 61.776 66.667 5.56 0.00 0.00 4.68
475 479 2.103340 GACGGAGCTCGCCTCTTC 59.897 66.667 7.83 0.00 43.89 2.87
483 487 1.009449 CTCGAATCCGACGGAGCTC 60.009 63.158 22.99 18.71 40.30 4.09
615 625 3.531207 CCGCGAGATCCAGAGCCA 61.531 66.667 8.23 0.00 0.00 4.75
1069 1114 0.609681 GGCGGATCTAGGACGAGGAT 60.610 60.000 0.00 0.00 0.00 3.24
1332 1386 1.880027 CAGGGTTAAAACGAGCTTGCT 59.120 47.619 0.00 0.00 0.00 3.91
1339 1393 2.224670 ACAGCATCCAGGGTTAAAACGA 60.225 45.455 0.00 0.00 0.00 3.85
1512 1573 3.309954 CGATTTAGGACTACAAAGCAGGC 59.690 47.826 0.00 0.00 0.00 4.85
1550 1611 4.532126 TCCATGTCTCCATCACACTAAAGT 59.468 41.667 0.00 0.00 0.00 2.66
1589 1650 3.056313 GCCAAATCGACCAGCCAGC 62.056 63.158 0.00 0.00 0.00 4.85
1693 1755 1.621814 AGAGTAAGCGTTAAGGCCACA 59.378 47.619 16.15 0.00 0.00 4.17
1705 1767 4.381411 ACAGTGGTGAAAGAAGAGTAAGC 58.619 43.478 0.00 0.00 0.00 3.09
1768 1830 3.965379 TTGAACAGTAGATGCCGGTAA 57.035 42.857 1.90 0.00 0.00 2.85
1774 1836 4.333649 TGCAGCTTATTGAACAGTAGATGC 59.666 41.667 0.00 0.00 0.00 3.91
1822 1884 4.787135 TGCATGGTATCTTATGGTTCCA 57.213 40.909 0.00 0.00 0.00 3.53
1832 1894 1.743772 GCGTGAGGTTGCATGGTATCT 60.744 52.381 0.00 0.00 0.00 1.98
1865 1927 2.882761 GCGTTAGGGAGTTTGAAAAGGT 59.117 45.455 0.00 0.00 0.00 3.50
1884 1946 1.136336 GTTTTACAAGCTGAGTCGGCG 60.136 52.381 18.16 0.00 41.21 6.46
2113 2183 8.405531 TGTTGCTTGAATAAAAGTAGATATGGC 58.594 33.333 0.00 0.00 0.00 4.40
2144 2214 9.955208 TGATGCTAAATTGCTAATTGTTATCAG 57.045 29.630 0.00 0.00 0.00 2.90
2388 2489 3.643237 TGGGACTCATAGGAAGTAGTGG 58.357 50.000 0.00 0.00 0.00 4.00
2451 2552 6.873076 GGCACAATATGAACAAGAAAAATGGA 59.127 34.615 0.00 0.00 0.00 3.41
2474 2575 4.960938 TGAAGGTGTCATATGATACAGGC 58.039 43.478 27.46 17.83 37.82 4.85
2579 2680 5.175673 GCCAAAATGCAGTCTGAACTTAAAC 59.824 40.000 3.32 0.00 31.71 2.01
2581 2682 4.340666 TGCCAAAATGCAGTCTGAACTTAA 59.659 37.500 3.32 0.00 36.04 1.85
2735 2838 2.301577 TTCCCTGCAAAACAAAACCG 57.698 45.000 0.00 0.00 0.00 4.44
3220 3323 9.242477 GGTGTACTTACTAGGAACGATAATTTC 57.758 37.037 0.00 0.00 0.00 2.17
3309 3412 5.117307 CAGTTCAAAGAACTGCAAAAACG 57.883 39.130 22.31 2.09 40.80 3.60
3414 3532 4.500375 GCCCCGACAGTAAACTCGTATATT 60.500 45.833 0.00 0.00 0.00 1.28
3420 3538 1.447314 GGCCCCGACAGTAAACTCG 60.447 63.158 0.00 0.00 0.00 4.18
3824 3945 9.606631 AGAAACCTAACAGCTAGAAATTATGAG 57.393 33.333 0.00 0.00 0.00 2.90
3830 3951 6.655425 GTGGAAGAAACCTAACAGCTAGAAAT 59.345 38.462 0.00 0.00 0.00 2.17
3940 4114 3.887716 ACGGCTACTTATTACCAGTCGAT 59.112 43.478 1.06 0.00 38.34 3.59
4002 4176 3.044156 AGATGGTCACCACATAGATGCT 58.956 45.455 0.00 0.00 35.80 3.79
4052 4226 0.100682 CAATCATGTGCTGCAGAGCC 59.899 55.000 20.43 4.19 45.57 4.70
4112 4287 1.271102 CAAGCCGAGGCCTAGATCTAC 59.729 57.143 15.38 0.00 43.17 2.59
4197 4372 1.812686 GCGTGCCCATATACCGAGGA 61.813 60.000 0.00 0.00 0.00 3.71
4198 4373 1.374252 GCGTGCCCATATACCGAGG 60.374 63.158 0.00 0.00 0.00 4.63
4201 4376 1.667830 CCTGCGTGCCCATATACCG 60.668 63.158 0.00 0.00 0.00 4.02
4210 4385 0.673644 ATGTAGAACACCTGCGTGCC 60.674 55.000 0.00 0.00 44.40 5.01
4213 4388 1.618837 ACAGATGTAGAACACCTGCGT 59.381 47.619 1.20 0.00 0.00 5.24
4215 4390 2.744202 CCAACAGATGTAGAACACCTGC 59.256 50.000 1.20 0.00 0.00 4.85
4223 4398 2.375174 AGGGCAAACCAACAGATGTAGA 59.625 45.455 0.00 0.00 43.89 2.59
4227 4402 1.474077 GCTAGGGCAAACCAACAGATG 59.526 52.381 0.00 0.00 43.89 2.90
4230 4405 1.620822 AAGCTAGGGCAAACCAACAG 58.379 50.000 0.00 0.00 43.89 3.16
4265 4440 0.446616 CACAATCCGTCGTCTCTCGA 59.553 55.000 0.00 0.00 46.83 4.04
4284 4459 6.420903 GGAAATTAACCAGTTTCAGTTTCAGC 59.579 38.462 2.61 0.00 36.34 4.26
4315 4490 6.831353 TGGGAAGAAATCTCAACTACAAACAA 59.169 34.615 0.00 0.00 34.88 2.83
4327 4502 4.133078 CAGTAGGCATGGGAAGAAATCTC 58.867 47.826 0.00 0.00 0.00 2.75
4329 4504 3.891049 ACAGTAGGCATGGGAAGAAATC 58.109 45.455 0.00 0.00 0.00 2.17
4349 4524 6.348786 GGTTCGGGTCCTTTTCAGTTTTATAC 60.349 42.308 0.00 0.00 0.00 1.47
4355 4610 1.213430 TGGTTCGGGTCCTTTTCAGTT 59.787 47.619 0.00 0.00 0.00 3.16
4375 4630 7.562454 TTGTGATCGGTTAGAAAAGAAAGTT 57.438 32.000 0.00 0.00 0.00 2.66
4379 4634 5.705441 AGCATTGTGATCGGTTAGAAAAGAA 59.295 36.000 0.00 0.00 0.00 2.52
4410 4666 0.323178 AAACAGCAGGGATGCTCAGG 60.323 55.000 0.00 0.00 44.30 3.86
4560 4817 4.078513 AGGCTACCTACCTTGGAGTAAGAT 60.079 45.833 0.00 0.00 32.85 2.40
4630 4887 0.593618 GCGATAGGAGCGAGATCACA 59.406 55.000 0.00 0.00 0.00 3.58
4765 5022 1.367471 CTCAACCTGTGGCGTCTCA 59.633 57.895 0.00 0.00 0.00 3.27
4769 5026 3.240134 ATCGCTCAACCTGTGGCGT 62.240 57.895 0.00 0.00 43.30 5.68
4773 5030 0.109086 AGACGATCGCTCAACCTGTG 60.109 55.000 16.60 0.00 0.00 3.66
4774 5031 0.171455 GAGACGATCGCTCAACCTGT 59.829 55.000 24.89 2.44 32.67 4.00
4805 5062 0.455410 CCTCTTCACTCTCTCAGGCG 59.545 60.000 0.00 0.00 0.00 5.52
4810 5067 0.175531 GCCTGCCTCTTCACTCTCTC 59.824 60.000 0.00 0.00 0.00 3.20
4811 5068 1.603236 CGCCTGCCTCTTCACTCTCT 61.603 60.000 0.00 0.00 0.00 3.10
4923 5183 0.684805 AAGGTAGAGAGGCCCTGTCG 60.685 60.000 0.00 0.00 0.00 4.35
4944 5204 1.649941 CGTTTTGCACGTGTGGTCG 60.650 57.895 18.38 11.85 44.49 4.79
4967 5227 3.181455 TGCAAACATACAGACACTGGAGT 60.181 43.478 0.00 0.00 35.51 3.85
4988 5248 4.752101 AGACTGAAAAAGAACGGAGACATG 59.248 41.667 0.00 0.00 0.00 3.21
5077 5337 2.224621 TGGAAAAGGCTCAGGAACTCTG 60.225 50.000 0.00 0.00 44.68 3.35
5150 5410 2.888594 AGCAACTATACGAACGCACAT 58.111 42.857 0.00 0.00 0.00 3.21
5155 5415 3.239026 CACCGTAAGCAACTATACGAACG 59.761 47.826 6.88 0.00 45.77 3.95
5171 5431 1.374505 GCCTACCAAACGCACCGTA 60.375 57.895 0.00 0.00 39.99 4.02
5172 5432 2.667199 GCCTACCAAACGCACCGT 60.667 61.111 0.00 0.00 43.97 4.83
5173 5433 2.358247 AGCCTACCAAACGCACCG 60.358 61.111 0.00 0.00 0.00 4.94
5174 5434 2.978018 GCAGCCTACCAAACGCACC 61.978 63.158 0.00 0.00 0.00 5.01
5175 5435 1.586154 ATGCAGCCTACCAAACGCAC 61.586 55.000 0.00 0.00 31.22 5.34
5212 5472 1.700404 CGTAAGCGACTATACGAACGC 59.300 52.381 0.00 0.00 45.77 4.84
5213 5473 2.285834 ACCGTAAGCGACTATACGAACG 60.286 50.000 6.88 0.00 45.77 3.95
5214 5474 3.031812 CACCGTAAGCGACTATACGAAC 58.968 50.000 6.88 0.00 45.77 3.95
5215 5475 2.539547 GCACCGTAAGCGACTATACGAA 60.540 50.000 6.88 0.00 45.77 3.85
5216 5476 1.003545 GCACCGTAAGCGACTATACGA 60.004 52.381 6.88 0.00 45.77 3.43
5217 5477 1.392756 GCACCGTAAGCGACTATACG 58.607 55.000 0.00 0.00 43.31 3.06
5226 5486 0.441145 CTACCAAACGCACCGTAAGC 59.559 55.000 0.00 0.00 39.99 3.09
5227 5487 1.073177 CCTACCAAACGCACCGTAAG 58.927 55.000 0.00 0.00 39.99 2.34
5228 5488 0.950071 GCCTACCAAACGCACCGTAA 60.950 55.000 0.00 0.00 39.99 3.18
5229 5489 1.374505 GCCTACCAAACGCACCGTA 60.375 57.895 0.00 0.00 39.99 4.02
5230 5490 2.667199 GCCTACCAAACGCACCGT 60.667 61.111 0.00 0.00 43.97 4.83
5231 5491 2.358247 AGCCTACCAAACGCACCG 60.358 61.111 0.00 0.00 0.00 4.94
5232 5492 2.978018 GCAGCCTACCAAACGCACC 61.978 63.158 0.00 0.00 0.00 5.01
5233 5493 1.586154 ATGCAGCCTACCAAACGCAC 61.586 55.000 0.00 0.00 31.22 5.34
5234 5494 0.035915 TATGCAGCCTACCAAACGCA 60.036 50.000 0.00 0.00 0.00 5.24
5259 5519 0.764369 ATCCTGCTCGGCCCTGATTA 60.764 55.000 0.00 0.00 0.00 1.75
5262 5522 3.473647 CATCCTGCTCGGCCCTGA 61.474 66.667 0.00 0.00 0.00 3.86
5267 5527 0.383231 CCAAATTCATCCTGCTCGGC 59.617 55.000 0.00 0.00 0.00 5.54
5360 5620 0.175989 GACCGATTCGAGCTTTCCCT 59.824 55.000 7.83 0.00 0.00 4.20
5396 5656 0.535102 CGTTTTCTGCCCCACTCAGT 60.535 55.000 0.00 0.00 33.48 3.41
5408 5668 0.949105 ATGCCGCGTCTTCGTTTTCT 60.949 50.000 4.92 0.00 39.49 2.52
5443 5703 3.933722 CATCTCCGCCCGCATCCT 61.934 66.667 0.00 0.00 0.00 3.24
5516 5778 3.615155 GCTAGAGGCAAGTGAGGAAATT 58.385 45.455 0.00 0.00 41.35 1.82
5528 5790 0.323999 TTGTCCTACGGCTAGAGGCA 60.324 55.000 3.81 0.00 44.01 4.75
5529 5791 0.822164 TTTGTCCTACGGCTAGAGGC 59.178 55.000 0.00 0.00 40.90 4.70
5554 5818 1.526455 GCCACCGGTACCAACAACA 60.526 57.895 6.87 0.00 0.00 3.33
5555 5819 2.609759 CGCCACCGGTACCAACAAC 61.610 63.158 6.87 0.00 0.00 3.32
5587 5854 4.147449 CGTCCCAGCCGCAGATCA 62.147 66.667 0.00 0.00 0.00 2.92
5632 5899 2.669569 CCGTTGCAGGGGAGTGTG 60.670 66.667 0.00 0.00 0.00 3.82
5743 6014 0.963962 TTACCAGCTTCGAGGTCGTT 59.036 50.000 0.00 0.00 39.31 3.85
5744 6015 0.526662 CTTACCAGCTTCGAGGTCGT 59.473 55.000 0.00 0.00 39.31 4.34
5781 6065 4.919168 CGAACGACCTAACACATAACAGAA 59.081 41.667 0.00 0.00 0.00 3.02
5875 6163 0.321122 CTGAACCAGAAGCTTCGCCT 60.321 55.000 20.43 6.93 32.44 5.52
5888 6176 1.153369 TATCAGCGCTGCCTGAACC 60.153 57.895 32.44 0.00 44.34 3.62
5980 6272 1.686325 CCCGGATCAACATCGGACCT 61.686 60.000 0.73 0.00 45.96 3.85
5992 6284 2.002505 TCCTCTCTTGATCCCGGATC 57.997 55.000 19.23 19.23 39.31 3.36
6033 6325 0.671472 GCAGGCCAAAAACCAGCATC 60.671 55.000 5.01 0.00 39.36 3.91
6034 6326 1.372307 GCAGGCCAAAAACCAGCAT 59.628 52.632 5.01 0.00 39.36 3.79
6035 6327 2.062777 TGCAGGCCAAAAACCAGCA 61.063 52.632 5.01 0.00 46.15 4.41
6040 6332 1.532437 GAGCAAATGCAGGCCAAAAAC 59.468 47.619 5.01 0.00 45.16 2.43
6041 6333 1.140452 TGAGCAAATGCAGGCCAAAAA 59.860 42.857 5.01 0.00 45.16 1.94
6042 6334 0.757512 TGAGCAAATGCAGGCCAAAA 59.242 45.000 5.01 0.00 45.16 2.44
6043 6335 0.757512 TTGAGCAAATGCAGGCCAAA 59.242 45.000 5.01 0.00 45.16 3.28
6044 6336 0.033781 GTTGAGCAAATGCAGGCCAA 59.966 50.000 5.01 3.75 45.16 4.52
6045 6337 1.667151 GTTGAGCAAATGCAGGCCA 59.333 52.632 5.01 0.00 45.16 5.36
6046 6338 1.079612 GGTTGAGCAAATGCAGGCC 60.080 57.895 8.28 0.00 45.16 5.19
6047 6339 0.389426 CTGGTTGAGCAAATGCAGGC 60.389 55.000 8.28 0.00 45.16 4.85
6048 6340 0.245539 CCTGGTTGAGCAAATGCAGG 59.754 55.000 8.28 0.60 45.16 4.85
6049 6341 0.389426 GCCTGGTTGAGCAAATGCAG 60.389 55.000 8.28 0.00 45.16 4.41
6050 6342 1.667151 GCCTGGTTGAGCAAATGCA 59.333 52.632 8.28 0.00 45.16 3.96
6051 6343 1.079612 GGCCTGGTTGAGCAAATGC 60.080 57.895 0.00 0.00 42.49 3.56
6052 6344 1.186917 TGGGCCTGGTTGAGCAAATG 61.187 55.000 4.53 0.00 0.00 2.32
6053 6345 0.471591 TTGGGCCTGGTTGAGCAAAT 60.472 50.000 4.53 0.00 0.00 2.32
6054 6346 1.075674 TTGGGCCTGGTTGAGCAAA 60.076 52.632 4.53 0.00 0.00 3.68
6055 6347 1.832167 GTTGGGCCTGGTTGAGCAA 60.832 57.895 4.53 0.00 0.00 3.91
6056 6348 2.203480 GTTGGGCCTGGTTGAGCA 60.203 61.111 4.53 0.00 0.00 4.26
6057 6349 2.116125 AGTTGGGCCTGGTTGAGC 59.884 61.111 4.53 0.00 0.00 4.26
6058 6350 0.607489 CTCAGTTGGGCCTGGTTGAG 60.607 60.000 4.53 9.11 33.14 3.02
6059 6351 1.059584 TCTCAGTTGGGCCTGGTTGA 61.060 55.000 4.53 2.79 33.14 3.18
6060 6352 0.890996 GTCTCAGTTGGGCCTGGTTG 60.891 60.000 4.53 0.00 33.14 3.77
6061 6353 1.352622 TGTCTCAGTTGGGCCTGGTT 61.353 55.000 4.53 0.00 33.14 3.67
6062 6354 1.352622 TTGTCTCAGTTGGGCCTGGT 61.353 55.000 4.53 0.00 33.14 4.00
6063 6355 0.607489 CTTGTCTCAGTTGGGCCTGG 60.607 60.000 4.53 0.00 33.14 4.45
6064 6356 0.109342 ACTTGTCTCAGTTGGGCCTG 59.891 55.000 4.53 0.00 0.00 4.85
6065 6357 1.729586 TACTTGTCTCAGTTGGGCCT 58.270 50.000 4.53 0.00 0.00 5.19
6066 6358 2.359900 CATACTTGTCTCAGTTGGGCC 58.640 52.381 0.00 0.00 0.00 5.80
6067 6359 1.740025 GCATACTTGTCTCAGTTGGGC 59.260 52.381 0.00 0.00 0.00 5.36
6068 6360 3.057969 TGCATACTTGTCTCAGTTGGG 57.942 47.619 0.00 0.00 0.00 4.12
6069 6361 5.437289 TTTTGCATACTTGTCTCAGTTGG 57.563 39.130 0.00 0.00 0.00 3.77
6070 6362 5.344128 GCATTTTGCATACTTGTCTCAGTTG 59.656 40.000 0.00 0.00 44.26 3.16
6071 6363 5.464168 GCATTTTGCATACTTGTCTCAGTT 58.536 37.500 0.00 0.00 44.26 3.16
6072 6364 4.378770 CGCATTTTGCATACTTGTCTCAGT 60.379 41.667 0.00 0.00 45.36 3.41
6073 6365 4.093514 CGCATTTTGCATACTTGTCTCAG 58.906 43.478 0.00 0.00 45.36 3.35
6074 6366 3.670359 GCGCATTTTGCATACTTGTCTCA 60.670 43.478 0.30 0.00 45.36 3.27
6075 6367 2.848302 GCGCATTTTGCATACTTGTCTC 59.152 45.455 0.30 0.00 45.36 3.36
6076 6368 2.489329 AGCGCATTTTGCATACTTGTCT 59.511 40.909 11.47 0.00 45.36 3.41
6077 6369 2.867429 AGCGCATTTTGCATACTTGTC 58.133 42.857 11.47 0.00 45.36 3.18
6078 6370 4.433186 TTAGCGCATTTTGCATACTTGT 57.567 36.364 11.47 0.00 45.36 3.16
6079 6371 5.760193 TTTTAGCGCATTTTGCATACTTG 57.240 34.783 11.47 0.00 45.36 3.16


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

AutoCloner maintained by Alex Coulton.