Multiple sequence alignment - TraesCS5D01G191000

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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 TraesCS5D01G191000 chr5D 100.000 4960 0 0 1 4960 293368578 293363619 0.000000e+00 9160.0
1 TraesCS5D01G191000 chr5A 96.516 2641 73 9 4 2635 386174848 386172218 0.000000e+00 4349.0
2 TraesCS5D01G191000 chr5A 95.641 1583 47 10 2795 4362 386172219 386170644 0.000000e+00 2521.0
3 TraesCS5D01G191000 chr5A 93.820 178 9 1 2627 2802 206730845 206731022 2.940000e-67 267.0
4 TraesCS5D01G191000 chr5B 96.879 2179 54 5 465 2635 334787337 334785165 0.000000e+00 3635.0
5 TraesCS5D01G191000 chr5B 95.544 1885 65 9 2851 4727 334784948 334783075 0.000000e+00 2998.0
6 TraesCS5D01G191000 chr5B 89.462 465 29 9 1 450 334788154 334787695 2.000000e-158 569.0
7 TraesCS5D01G191000 chr5B 96.364 55 2 0 2795 2849 334785166 334785112 1.900000e-14 91.6
8 TraesCS5D01G191000 chr6A 94.492 236 12 1 4723 4958 428284245 428284011 3.650000e-96 363.0
9 TraesCS5D01G191000 chr4D 94.850 233 11 1 4729 4960 179880346 179880114 3.650000e-96 363.0
10 TraesCS5D01G191000 chr4D 86.694 248 25 5 4719 4960 488483209 488482964 8.180000e-68 268.0
11 TraesCS5D01G191000 chr6B 93.333 240 14 1 4723 4960 454740459 454740698 2.200000e-93 353.0
12 TraesCS5D01G191000 chr7A 90.756 238 22 0 4723 4960 183304281 183304044 8.010000e-83 318.0
13 TraesCS5D01G191000 chr7A 93.642 173 9 1 2634 2804 115807687 115807515 1.770000e-64 257.0
14 TraesCS5D01G191000 chr7D 88.382 241 24 2 4719 4958 199600357 199600594 2.260000e-73 287.0
15 TraesCS5D01G191000 chr7D 95.808 167 5 1 2633 2797 192936019 192936185 8.180000e-68 268.0
16 TraesCS5D01G191000 chr7D 88.210 229 21 5 4720 4944 498726947 498726721 8.180000e-68 268.0
17 TraesCS5D01G191000 chr7D 92.308 182 10 3 2617 2796 535309675 535309854 6.370000e-64 255.0
18 TraesCS5D01G191000 chr6D 93.443 183 9 2 2628 2807 270689516 270689334 8.180000e-68 268.0
19 TraesCS5D01G191000 chr6D 92.896 183 10 2 2628 2807 270587541 270587359 3.810000e-66 263.0
20 TraesCS5D01G191000 chr6D 93.296 179 10 1 2633 2809 392897140 392896962 3.810000e-66 263.0
21 TraesCS5D01G191000 chr2A 94.318 176 7 2 2624 2796 746757165 746756990 2.940000e-67 267.0
22 TraesCS5D01G191000 chr2A 84.454 238 31 6 4723 4960 235311803 235312034 3.860000e-56 230.0
23 TraesCS5D01G191000 chr2D 92.818 181 10 2 2625 2803 446317634 446317813 4.930000e-65 259.0
24 TraesCS5D01G191000 chr2D 82.105 95 17 0 3353 3447 9626455 9626361 1.140000e-11 82.4
25 TraesCS5D01G191000 chr3D 84.034 238 34 4 4723 4960 267264620 267264387 5.000000e-55 226.0


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 TraesCS5D01G191000 chr5D 293363619 293368578 4959 True 9160.0 9160 100.00000 1 4960 1 chr5D.!!$R1 4959
1 TraesCS5D01G191000 chr5A 386170644 386174848 4204 True 3435.0 4349 96.07850 4 4362 2 chr5A.!!$R1 4358
2 TraesCS5D01G191000 chr5B 334783075 334788154 5079 True 1823.4 3635 94.56225 1 4727 4 chr5B.!!$R1 4726

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
37 38 0.977395 AGTAAGAAGCAAGCGAGGGT 59.023 50.000 0.00 0.00 0.00 4.34 F
555 913 1.072173 TCACCATGTTCTGTGTCCCTG 59.928 52.381 0.00 0.00 34.14 4.45 F
2289 2661 1.904287 TAATTGGGTGGTGTGACAGC 58.096 50.000 8.00 8.00 38.10 4.40 F
2906 3337 0.034380 GAAGGAACCTAGGGCCAACC 60.034 60.000 21.09 12.78 40.67 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1956 1.067060 CTGATCTCCGCGGTCATTGTA 59.933 52.381 27.15 1.93 0.00 2.41 R
2357 2729 2.023788 GCCATTTTAGCAGCCTGCCTA 61.024 52.381 14.25 2.35 46.52 3.93 R
3323 3764 0.179936 GCTCCCACTCTGAATGGAGG 59.820 60.000 6.74 0.11 43.74 4.30 R
4760 5211 0.031178 GGTTGCTCTGTGGCAGTTTG 59.969 55.000 0.00 0.00 43.39 2.93 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
37 38 0.977395 AGTAAGAAGCAAGCGAGGGT 59.023 50.000 0.00 0.00 0.00 4.34
104 105 1.972872 CCTGGTTATGGTCTCATGGC 58.027 55.000 0.00 0.00 34.96 4.40
452 465 7.504924 TCGAGAAATTGTTTCATGTTAAGGT 57.495 32.000 5.36 0.00 42.10 3.50
491 847 7.942341 TGGGTGTAAATGTAGTCTGAAGAAATT 59.058 33.333 0.00 0.00 0.00 1.82
539 897 6.560253 TTAGTTTTTGCTTCTGAGATCACC 57.440 37.500 0.00 0.00 0.00 4.02
552 910 3.265791 GAGATCACCATGTTCTGTGTCC 58.734 50.000 0.00 0.00 34.14 4.02
553 911 2.026822 AGATCACCATGTTCTGTGTCCC 60.027 50.000 0.00 0.00 34.14 4.46
555 913 1.072173 TCACCATGTTCTGTGTCCCTG 59.928 52.381 0.00 0.00 34.14 4.45
705 1063 2.415625 CGAACTTTCTCCCACCTCTACG 60.416 54.545 0.00 0.00 0.00 3.51
879 1243 2.325484 GGGTGGTTTGAAAAGGTCCAT 58.675 47.619 0.00 0.00 0.00 3.41
1065 1431 6.700352 CACCTTATTGTTTTCCATCCATGTT 58.300 36.000 0.00 0.00 0.00 2.71
1070 1436 8.657387 TTATTGTTTTCCATCCATGTTCCTTA 57.343 30.769 0.00 0.00 0.00 2.69
1104 1470 5.365314 ACTCTCCTTCAACTTCAACTTCTCT 59.635 40.000 0.00 0.00 0.00 3.10
1123 1489 2.041922 ATCCCGGCTCCTACTGCA 60.042 61.111 0.00 0.00 0.00 4.41
1167 1533 4.567318 GGCGATGCCTTCTTCCAT 57.433 55.556 0.00 0.00 46.69 3.41
1590 1956 8.968969 CCTGATAAGAAACTTACACTAGGTACT 58.031 37.037 0.00 0.00 46.37 2.73
2184 2556 3.925379 TGTTGCGATAAAGAAGCTCTCA 58.075 40.909 0.00 0.00 0.00 3.27
2289 2661 1.904287 TAATTGGGTGGTGTGACAGC 58.096 50.000 8.00 8.00 38.10 4.40
2428 2800 8.850452 GTTTCTTGCGGAATTTCTTACATTTAG 58.150 33.333 0.00 0.00 33.53 1.85
2575 2948 9.107177 CTTATTAGTCTGCAGATCAATGTTTCT 57.893 33.333 21.47 11.10 0.00 2.52
2648 3076 1.486211 CACATACTCCCTCCGTTCCT 58.514 55.000 0.00 0.00 0.00 3.36
2649 3077 1.831736 CACATACTCCCTCCGTTCCTT 59.168 52.381 0.00 0.00 0.00 3.36
2654 3082 6.014499 CACATACTCCCTCCGTTCCTTAATAT 60.014 42.308 0.00 0.00 0.00 1.28
2663 3091 7.122204 CCCTCCGTTCCTTAATATTTGTCTTTT 59.878 37.037 0.00 0.00 0.00 2.27
2700 3128 4.710865 TGGACTACCACAAACGGATGTATA 59.289 41.667 0.00 0.00 41.77 1.47
2746 3176 4.875544 TTCATTTTGCTCCGTATGTAGC 57.124 40.909 0.00 0.00 39.25 3.58
2774 3204 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2795 3225 9.847224 GACAAATATTTAAGAATGGAGGGAGTA 57.153 33.333 0.00 0.00 0.00 2.59
2796 3226 9.853177 ACAAATATTTAAGAATGGAGGGAGTAG 57.147 33.333 0.00 0.00 0.00 2.57
2797 3227 9.853177 CAAATATTTAAGAATGGAGGGAGTAGT 57.147 33.333 0.00 0.00 0.00 2.73
2800 3230 7.757242 ATTTAAGAATGGAGGGAGTAGTTCT 57.243 36.000 0.00 0.00 0.00 3.01
2801 3231 7.569599 TTTAAGAATGGAGGGAGTAGTTCTT 57.430 36.000 0.00 0.00 38.82 2.52
2802 3232 7.569599 TTAAGAATGGAGGGAGTAGTTCTTT 57.430 36.000 3.84 0.00 37.21 2.52
2803 3233 6.455690 AAGAATGGAGGGAGTAGTTCTTTT 57.544 37.500 0.00 0.00 33.50 2.27
2804 3234 5.810095 AGAATGGAGGGAGTAGTTCTTTTG 58.190 41.667 0.00 0.00 0.00 2.44
2805 3235 3.418684 TGGAGGGAGTAGTTCTTTTGC 57.581 47.619 0.00 0.00 0.00 3.68
2806 3236 2.979678 TGGAGGGAGTAGTTCTTTTGCT 59.020 45.455 0.00 0.00 0.00 3.91
2807 3237 3.244561 TGGAGGGAGTAGTTCTTTTGCTG 60.245 47.826 0.00 0.00 0.00 4.41
2808 3238 3.244596 GGAGGGAGTAGTTCTTTTGCTGT 60.245 47.826 0.00 0.00 0.00 4.40
2809 3239 4.020485 GGAGGGAGTAGTTCTTTTGCTGTA 60.020 45.833 0.00 0.00 0.00 2.74
2810 3240 5.153950 AGGGAGTAGTTCTTTTGCTGTAG 57.846 43.478 0.00 0.00 0.00 2.74
2811 3241 3.685272 GGGAGTAGTTCTTTTGCTGTAGC 59.315 47.826 0.00 0.00 42.50 3.58
2858 3288 5.832539 AGGGCTTACATAACAGATAGCAT 57.167 39.130 0.00 0.00 0.00 3.79
2892 3322 7.592736 TCTACCTATTGGTATCTTGAGAAGGA 58.407 38.462 6.51 0.00 46.67 3.36
2894 3324 6.890293 ACCTATTGGTATCTTGAGAAGGAAC 58.110 40.000 0.00 0.00 46.43 3.62
2896 3326 6.100424 CCTATTGGTATCTTGAGAAGGAACCT 59.900 42.308 0.00 0.00 35.79 3.50
2898 3328 6.546428 TTGGTATCTTGAGAAGGAACCTAG 57.454 41.667 0.00 0.00 35.79 3.02
2899 3329 4.962995 TGGTATCTTGAGAAGGAACCTAGG 59.037 45.833 7.41 7.41 35.79 3.02
2906 3337 0.034380 GAAGGAACCTAGGGCCAACC 60.034 60.000 21.09 12.78 40.67 3.77
2955 3391 3.801114 AGGCTTGAAAACCAACAGAAC 57.199 42.857 0.00 0.00 0.00 3.01
2996 3432 6.044682 AGAGAAAGTGAACCATTTGCAAAAG 58.955 36.000 17.19 12.00 0.00 2.27
2997 3433 5.976458 AGAAAGTGAACCATTTGCAAAAGA 58.024 33.333 17.19 0.00 0.00 2.52
3142 3578 4.564406 CCAACAATTACTCTCTGCCACTCT 60.564 45.833 0.00 0.00 0.00 3.24
3143 3579 5.337571 CCAACAATTACTCTCTGCCACTCTA 60.338 44.000 0.00 0.00 0.00 2.43
3163 3601 6.613271 ACTCTATGTCTTCCCTGATGTTACAT 59.387 38.462 0.00 0.00 0.00 2.29
3171 3609 4.588899 TCCCTGATGTTACATTTGACTGG 58.411 43.478 0.00 0.44 0.00 4.00
3182 3620 8.861086 TGTTACATTTGACTGGCCTTTTTATTA 58.139 29.630 3.32 0.00 0.00 0.98
3183 3621 9.869757 GTTACATTTGACTGGCCTTTTTATTAT 57.130 29.630 3.32 0.00 0.00 1.28
3184 3622 9.868277 TTACATTTGACTGGCCTTTTTATTATG 57.132 29.630 3.32 1.21 0.00 1.90
3266 3704 4.595762 AAGTACTTCACTTGGCTAACGA 57.404 40.909 1.12 0.00 46.01 3.85
3267 3705 4.803098 AGTACTTCACTTGGCTAACGAT 57.197 40.909 0.00 0.00 31.59 3.73
3268 3706 5.909621 AGTACTTCACTTGGCTAACGATA 57.090 39.130 0.00 0.00 31.59 2.92
3302 3743 6.899089 TGACAGGTACAATATCATCATTGGT 58.101 36.000 0.00 0.00 39.71 3.67
3323 3764 2.584694 GGCTCTGCTCTGCGCTAC 60.585 66.667 9.73 0.00 40.11 3.58
3506 3947 2.159448 CGGATACATCGATCCTGAGCTC 60.159 54.545 6.82 6.82 42.97 4.09
4248 4698 4.916041 TCATCATTTCCCAGAGTCAAGT 57.084 40.909 0.00 0.00 0.00 3.16
4251 4701 6.409704 TCATCATTTCCCAGAGTCAAGTTAG 58.590 40.000 0.00 0.00 0.00 2.34
4264 4714 8.669243 CAGAGTCAAGTTAGGGTTGAAATAATC 58.331 37.037 0.00 0.00 35.71 1.75
4420 4870 4.003648 CCCTGCGAAAACTGATAACTCTT 58.996 43.478 0.00 0.00 0.00 2.85
4445 4895 4.553756 TCTGTTCGATCCAGATCTTACG 57.446 45.455 10.36 0.00 34.12 3.18
4451 4901 3.058155 TCGATCCAGATCTTACGCTTAGC 60.058 47.826 6.12 0.00 35.72 3.09
4454 4904 4.244425 TCCAGATCTTACGCTTAGCATC 57.756 45.455 4.70 0.00 0.00 3.91
4458 4908 4.045104 AGATCTTACGCTTAGCATCAACG 58.955 43.478 4.70 0.00 0.00 4.10
4474 4924 7.810658 AGCATCAACGCCATCTTTATTATAAG 58.189 34.615 0.00 0.00 0.00 1.73
4501 4951 3.186409 AGAATCGTTTCGGTTGTGTGATG 59.814 43.478 0.72 0.00 36.93 3.07
4517 4967 0.525668 GATGTACACCTCACGGCGAG 60.526 60.000 16.62 5.72 41.89 5.03
4529 4979 0.467474 ACGGCGAGGGTCAGATATGA 60.467 55.000 16.62 0.00 0.00 2.15
4543 4993 6.183361 GGTCAGATATGACACATACCCTTTCT 60.183 42.308 21.27 0.00 40.38 2.52
4573 5023 4.078537 CTCTCTTTCTCTCTCACTGACCA 58.921 47.826 0.00 0.00 0.00 4.02
4631 5082 5.341872 CATTGCCATGGAAATAGGTGAAA 57.658 39.130 18.17 0.00 0.00 2.69
4654 5105 2.577593 GAGACGGGTGGTGCTACC 59.422 66.667 0.00 0.00 40.10 3.18
4670 5121 1.294426 TACCGTCCCTCTCCATCCCT 61.294 60.000 0.00 0.00 0.00 4.20
4685 5136 3.322466 CCTGAGCCCGTGGACCTT 61.322 66.667 0.00 0.00 0.00 3.50
4709 5160 0.606673 GGTGCAAACCCTCACTCCTC 60.607 60.000 0.00 0.00 33.91 3.71
4710 5161 0.606673 GTGCAAACCCTCACTCCTCC 60.607 60.000 0.00 0.00 0.00 4.30
4724 5175 2.833582 CTCCGCGGCCTCTCCTTA 60.834 66.667 23.51 0.00 0.00 2.69
4727 5178 2.049985 CGCGGCCTCTCCTTATCG 60.050 66.667 0.00 0.00 0.00 2.92
4728 5179 2.552819 CGCGGCCTCTCCTTATCGA 61.553 63.158 0.00 0.00 0.00 3.59
4729 5180 1.740285 GCGGCCTCTCCTTATCGAA 59.260 57.895 0.00 0.00 0.00 3.71
4730 5181 0.104304 GCGGCCTCTCCTTATCGAAA 59.896 55.000 0.00 0.00 0.00 3.46
4731 5182 1.472728 GCGGCCTCTCCTTATCGAAAA 60.473 52.381 0.00 0.00 0.00 2.29
4732 5183 2.901249 CGGCCTCTCCTTATCGAAAAA 58.099 47.619 0.00 0.00 0.00 1.94
4733 5184 2.866762 CGGCCTCTCCTTATCGAAAAAG 59.133 50.000 0.00 0.00 0.00 2.27
4734 5185 3.206964 GGCCTCTCCTTATCGAAAAAGG 58.793 50.000 19.15 19.15 44.17 3.11
4735 5186 2.614520 GCCTCTCCTTATCGAAAAAGGC 59.385 50.000 20.01 13.34 42.79 4.35
4736 5187 3.682999 GCCTCTCCTTATCGAAAAAGGCT 60.683 47.826 20.01 0.00 43.67 4.58
4737 5188 4.518249 CCTCTCCTTATCGAAAAAGGCTT 58.482 43.478 20.01 0.00 42.79 4.35
4738 5189 4.944317 CCTCTCCTTATCGAAAAAGGCTTT 59.056 41.667 20.01 6.68 42.79 3.51
4739 5190 5.065346 CCTCTCCTTATCGAAAAAGGCTTTC 59.935 44.000 20.01 0.41 42.79 2.62
4751 5202 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
4752 5203 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
4753 5204 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
4754 5205 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
4755 5206 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
4756 5207 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
4757 5208 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
4758 5209 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
4771 5222 8.755696 CTTTATAAATAAAGCAAACTGCCACA 57.244 30.769 9.01 0.00 46.52 4.17
4772 5223 8.755696 TTTATAAATAAAGCAAACTGCCACAG 57.244 30.769 0.00 0.00 46.52 3.66
4773 5224 4.935352 AAATAAAGCAAACTGCCACAGA 57.065 36.364 0.78 0.00 46.52 3.41
4774 5225 4.510038 AATAAAGCAAACTGCCACAGAG 57.490 40.909 0.78 0.00 46.52 3.35
4775 5226 0.386838 AAAGCAAACTGCCACAGAGC 59.613 50.000 0.78 2.91 46.52 4.09
4776 5227 0.752743 AAGCAAACTGCCACAGAGCA 60.753 50.000 0.78 0.00 46.52 4.26
4777 5228 0.752743 AGCAAACTGCCACAGAGCAA 60.753 50.000 0.78 0.00 46.52 3.91
4778 5229 0.595825 GCAAACTGCCACAGAGCAAC 60.596 55.000 0.78 0.00 43.52 4.17
4779 5230 0.031178 CAAACTGCCACAGAGCAACC 59.969 55.000 0.78 0.00 43.52 3.77
4780 5231 0.395586 AAACTGCCACAGAGCAACCA 60.396 50.000 0.78 0.00 43.52 3.67
4781 5232 0.178981 AACTGCCACAGAGCAACCAT 60.179 50.000 0.78 0.00 43.52 3.55
4782 5233 0.692476 ACTGCCACAGAGCAACCATA 59.308 50.000 0.78 0.00 43.52 2.74
4783 5234 1.089920 CTGCCACAGAGCAACCATAC 58.910 55.000 0.00 0.00 43.52 2.39
4784 5235 0.399833 TGCCACAGAGCAACCATACA 59.600 50.000 0.00 0.00 40.56 2.29
4785 5236 1.202867 TGCCACAGAGCAACCATACAA 60.203 47.619 0.00 0.00 40.56 2.41
4786 5237 1.470098 GCCACAGAGCAACCATACAAG 59.530 52.381 0.00 0.00 0.00 3.16
4787 5238 2.086869 CCACAGAGCAACCATACAAGG 58.913 52.381 0.00 0.00 0.00 3.61
4788 5239 2.290260 CCACAGAGCAACCATACAAGGA 60.290 50.000 0.00 0.00 0.00 3.36
4789 5240 2.744202 CACAGAGCAACCATACAAGGAC 59.256 50.000 0.00 0.00 0.00 3.85
4790 5241 2.639839 ACAGAGCAACCATACAAGGACT 59.360 45.455 0.00 0.00 0.00 3.85
4791 5242 3.838317 ACAGAGCAACCATACAAGGACTA 59.162 43.478 0.00 0.00 0.00 2.59
4792 5243 4.081420 ACAGAGCAACCATACAAGGACTAG 60.081 45.833 0.00 0.00 0.00 2.57
4793 5244 4.081420 CAGAGCAACCATACAAGGACTAGT 60.081 45.833 0.00 0.00 0.00 2.57
4794 5245 4.160626 AGAGCAACCATACAAGGACTAGTC 59.839 45.833 14.87 14.87 0.00 2.59
4807 5258 3.728076 GACTAGTCCACAACTCACACA 57.272 47.619 12.13 0.00 39.55 3.72
4808 5259 3.381949 GACTAGTCCACAACTCACACAC 58.618 50.000 12.13 0.00 39.55 3.82
4809 5260 2.102588 ACTAGTCCACAACTCACACACC 59.897 50.000 0.00 0.00 39.55 4.16
4810 5261 0.180406 AGTCCACAACTCACACACCC 59.820 55.000 0.00 0.00 30.02 4.61
4811 5262 0.107410 GTCCACAACTCACACACCCA 60.107 55.000 0.00 0.00 0.00 4.51
4812 5263 0.107410 TCCACAACTCACACACCCAC 60.107 55.000 0.00 0.00 0.00 4.61
4813 5264 1.436195 CCACAACTCACACACCCACG 61.436 60.000 0.00 0.00 0.00 4.94
4814 5265 0.742990 CACAACTCACACACCCACGT 60.743 55.000 0.00 0.00 0.00 4.49
4815 5266 0.461339 ACAACTCACACACCCACGTC 60.461 55.000 0.00 0.00 0.00 4.34
4816 5267 0.179084 CAACTCACACACCCACGTCT 60.179 55.000 0.00 0.00 0.00 4.18
4817 5268 0.104304 AACTCACACACCCACGTCTC 59.896 55.000 0.00 0.00 0.00 3.36
4818 5269 1.040893 ACTCACACACCCACGTCTCA 61.041 55.000 0.00 0.00 0.00 3.27
4819 5270 0.597637 CTCACACACCCACGTCTCAC 60.598 60.000 0.00 0.00 0.00 3.51
4821 5272 2.122797 ACACACCCACGTCTCACGA 61.123 57.895 2.48 0.00 46.05 4.35
4822 5273 1.660575 CACACCCACGTCTCACGAC 60.661 63.158 2.48 0.00 46.05 4.34
4823 5274 2.122797 ACACCCACGTCTCACGACA 61.123 57.895 2.48 0.00 46.05 4.35
4824 5275 1.066752 CACCCACGTCTCACGACAA 59.933 57.895 2.48 0.00 46.05 3.18
4825 5276 0.319555 CACCCACGTCTCACGACAAT 60.320 55.000 2.48 0.00 46.05 2.71
4826 5277 1.068125 CACCCACGTCTCACGACAATA 60.068 52.381 2.48 0.00 46.05 1.90
4827 5278 1.614903 ACCCACGTCTCACGACAATAA 59.385 47.619 2.48 0.00 46.05 1.40
4828 5279 2.259618 CCCACGTCTCACGACAATAAG 58.740 52.381 2.48 0.00 46.05 1.73
4829 5280 2.352421 CCCACGTCTCACGACAATAAGT 60.352 50.000 2.48 0.00 46.05 2.24
4830 5281 3.119743 CCCACGTCTCACGACAATAAGTA 60.120 47.826 2.48 0.00 46.05 2.24
4831 5282 3.850273 CCACGTCTCACGACAATAAGTAC 59.150 47.826 2.48 0.00 46.05 2.73
4832 5283 4.469552 CACGTCTCACGACAATAAGTACA 58.530 43.478 2.48 0.00 46.05 2.90
4833 5284 4.913345 CACGTCTCACGACAATAAGTACAA 59.087 41.667 2.48 0.00 46.05 2.41
4834 5285 5.400188 CACGTCTCACGACAATAAGTACAAA 59.600 40.000 2.48 0.00 46.05 2.83
4835 5286 5.978919 ACGTCTCACGACAATAAGTACAAAA 59.021 36.000 2.48 0.00 46.05 2.44
4836 5287 6.143438 ACGTCTCACGACAATAAGTACAAAAG 59.857 38.462 2.48 0.00 46.05 2.27
4837 5288 6.399669 CGTCTCACGACAATAAGTACAAAAGG 60.400 42.308 0.00 0.00 46.05 3.11
4838 5289 6.423001 GTCTCACGACAATAAGTACAAAAGGT 59.577 38.462 0.00 0.00 39.98 3.50
4839 5290 6.987992 TCTCACGACAATAAGTACAAAAGGTT 59.012 34.615 0.00 0.00 0.00 3.50
4840 5291 7.170320 TCTCACGACAATAAGTACAAAAGGTTC 59.830 37.037 0.00 0.00 0.00 3.62
4841 5292 6.987992 TCACGACAATAAGTACAAAAGGTTCT 59.012 34.615 0.00 0.00 0.00 3.01
4842 5293 7.042321 TCACGACAATAAGTACAAAAGGTTCTG 60.042 37.037 0.00 0.00 0.00 3.02
4843 5294 6.764560 ACGACAATAAGTACAAAAGGTTCTGT 59.235 34.615 0.00 0.00 0.00 3.41
4844 5295 7.281549 ACGACAATAAGTACAAAAGGTTCTGTT 59.718 33.333 0.00 0.00 0.00 3.16
4845 5296 7.586300 CGACAATAAGTACAAAAGGTTCTGTTG 59.414 37.037 0.00 0.00 35.04 3.33
4846 5297 8.514330 ACAATAAGTACAAAAGGTTCTGTTGA 57.486 30.769 4.98 0.00 32.81 3.18
4847 5298 8.621286 ACAATAAGTACAAAAGGTTCTGTTGAG 58.379 33.333 4.98 0.00 32.81 3.02
4848 5299 7.745620 ATAAGTACAAAAGGTTCTGTTGAGG 57.254 36.000 4.98 0.00 32.81 3.86
4849 5300 4.461198 AGTACAAAAGGTTCTGTTGAGGG 58.539 43.478 4.98 0.00 32.81 4.30
4850 5301 2.031870 ACAAAAGGTTCTGTTGAGGGC 58.968 47.619 4.98 0.00 32.81 5.19
4851 5302 2.031120 CAAAAGGTTCTGTTGAGGGCA 58.969 47.619 0.00 0.00 30.76 5.36
4852 5303 1.692411 AAAGGTTCTGTTGAGGGCAC 58.308 50.000 0.00 0.00 0.00 5.01
4853 5304 0.550914 AAGGTTCTGTTGAGGGCACA 59.449 50.000 0.00 0.00 0.00 4.57
4854 5305 0.109342 AGGTTCTGTTGAGGGCACAG 59.891 55.000 0.00 0.00 0.00 3.66
4855 5306 1.518903 GGTTCTGTTGAGGGCACAGC 61.519 60.000 0.00 0.00 0.00 4.40
4856 5307 0.536006 GTTCTGTTGAGGGCACAGCT 60.536 55.000 0.00 0.00 0.00 4.24
4857 5308 0.250467 TTCTGTTGAGGGCACAGCTC 60.250 55.000 0.00 0.00 0.00 4.09
4858 5309 1.071987 CTGTTGAGGGCACAGCTCA 59.928 57.895 0.00 0.00 0.00 4.26
4859 5310 0.535780 CTGTTGAGGGCACAGCTCAA 60.536 55.000 0.00 0.00 35.01 3.02
4860 5311 1.952263 GTTGAGGGCACAGCTCAAC 59.048 57.895 15.36 15.36 45.16 3.18
4861 5312 1.531259 TTGAGGGCACAGCTCAACA 59.469 52.632 0.00 0.00 33.06 3.33
4862 5313 0.106769 TTGAGGGCACAGCTCAACAA 60.107 50.000 0.00 0.00 33.06 2.83
4863 5314 0.535780 TGAGGGCACAGCTCAACAAG 60.536 55.000 0.00 0.00 0.00 3.16
4873 5324 2.307934 GCTCAACAAGCCCAAACAAA 57.692 45.000 0.00 0.00 45.92 2.83
4874 5325 2.626840 GCTCAACAAGCCCAAACAAAA 58.373 42.857 0.00 0.00 45.92 2.44
4875 5326 2.609002 GCTCAACAAGCCCAAACAAAAG 59.391 45.455 0.00 0.00 45.92 2.27
4876 5327 3.678529 GCTCAACAAGCCCAAACAAAAGA 60.679 43.478 0.00 0.00 45.92 2.52
4877 5328 4.502962 CTCAACAAGCCCAAACAAAAGAA 58.497 39.130 0.00 0.00 0.00 2.52
4878 5329 4.899502 TCAACAAGCCCAAACAAAAGAAA 58.100 34.783 0.00 0.00 0.00 2.52
4879 5330 5.308825 TCAACAAGCCCAAACAAAAGAAAA 58.691 33.333 0.00 0.00 0.00 2.29
4880 5331 5.765182 TCAACAAGCCCAAACAAAAGAAAAA 59.235 32.000 0.00 0.00 0.00 1.94
4881 5332 5.878332 ACAAGCCCAAACAAAAGAAAAAG 57.122 34.783 0.00 0.00 0.00 2.27
4882 5333 5.555966 ACAAGCCCAAACAAAAGAAAAAGA 58.444 33.333 0.00 0.00 0.00 2.52
4883 5334 6.000840 ACAAGCCCAAACAAAAGAAAAAGAA 58.999 32.000 0.00 0.00 0.00 2.52
4884 5335 6.658816 ACAAGCCCAAACAAAAGAAAAAGAAT 59.341 30.769 0.00 0.00 0.00 2.40
4885 5336 6.682423 AGCCCAAACAAAAGAAAAAGAATG 57.318 33.333 0.00 0.00 0.00 2.67
4886 5337 5.589855 AGCCCAAACAAAAGAAAAAGAATGG 59.410 36.000 0.00 0.00 0.00 3.16
4887 5338 5.733091 GCCCAAACAAAAGAAAAAGAATGGC 60.733 40.000 0.00 0.00 0.00 4.40
4888 5339 5.221028 CCCAAACAAAAGAAAAAGAATGGCC 60.221 40.000 0.00 0.00 0.00 5.36
4889 5340 5.500825 CAAACAAAAGAAAAAGAATGGCCG 58.499 37.500 0.00 0.00 0.00 6.13
4890 5341 3.727726 ACAAAAGAAAAAGAATGGCCGG 58.272 40.909 0.00 0.00 0.00 6.13
4891 5342 3.066380 CAAAAGAAAAAGAATGGCCGGG 58.934 45.455 2.18 0.00 0.00 5.73
4892 5343 1.266178 AAGAAAAAGAATGGCCGGGG 58.734 50.000 2.18 0.00 0.00 5.73
4893 5344 0.614697 AGAAAAAGAATGGCCGGGGG 60.615 55.000 2.18 0.00 0.00 5.40
4894 5345 0.613572 GAAAAAGAATGGCCGGGGGA 60.614 55.000 2.18 0.00 0.00 4.81
4895 5346 0.614697 AAAAAGAATGGCCGGGGGAG 60.615 55.000 2.18 0.00 0.00 4.30
4896 5347 2.514516 AAAAGAATGGCCGGGGGAGG 62.515 60.000 2.18 0.00 0.00 4.30
4922 5373 4.963428 CGCGCCCGACCCCTAATC 62.963 72.222 0.00 0.00 36.29 1.75
4923 5374 4.620937 GCGCCCGACCCCTAATCC 62.621 72.222 0.00 0.00 0.00 3.01
4924 5375 4.295119 CGCCCGACCCCTAATCCG 62.295 72.222 0.00 0.00 0.00 4.18
4925 5376 3.937447 GCCCGACCCCTAATCCGG 61.937 72.222 0.00 0.00 41.47 5.14
4926 5377 3.937447 CCCGACCCCTAATCCGGC 61.937 72.222 0.00 0.00 40.56 6.13
4927 5378 2.842936 CCGACCCCTAATCCGGCT 60.843 66.667 0.00 0.00 35.29 5.52
4928 5379 2.735237 CGACCCCTAATCCGGCTC 59.265 66.667 0.00 0.00 0.00 4.70
4929 5380 2.735237 GACCCCTAATCCGGCTCG 59.265 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
230 232 9.860898 GTTTAACAGCAATAAATCCAGAAATCT 57.139 29.630 0.00 0.00 0.00 2.40
452 465 7.978925 ACATTTACACCCAAATTTTATTCCCA 58.021 30.769 0.00 0.00 0.00 4.37
500 856 9.476202 GCAAAAACTAAACATCTGTTTTAGGAT 57.524 29.630 13.06 0.00 45.07 3.24
501 857 8.691797 AGCAAAAACTAAACATCTGTTTTAGGA 58.308 29.630 13.06 0.00 45.07 2.94
502 858 8.871686 AGCAAAAACTAAACATCTGTTTTAGG 57.128 30.769 13.06 7.35 45.07 2.69
505 861 8.872845 CAGAAGCAAAAACTAAACATCTGTTTT 58.127 29.630 13.06 0.00 45.07 2.43
539 897 3.244561 ACCTTACAGGGACACAGAACATG 60.245 47.826 0.00 0.00 40.58 3.21
552 910 4.154195 CAGAATTTTCCGACACCTTACAGG 59.846 45.833 0.00 0.00 42.49 4.00
553 911 4.755123 ACAGAATTTTCCGACACCTTACAG 59.245 41.667 0.00 0.00 0.00 2.74
555 913 5.237779 TGAACAGAATTTTCCGACACCTTAC 59.762 40.000 0.00 0.00 0.00 2.34
561 919 6.206438 TGATGAATGAACAGAATTTTCCGACA 59.794 34.615 0.00 0.00 0.00 4.35
705 1063 0.819582 AAATACATGGGCAGTGCAGC 59.180 50.000 18.61 0.00 0.00 5.25
1042 1408 6.070824 GGAACATGGATGGAAAACAATAAGGT 60.071 38.462 0.00 0.00 0.00 3.50
1065 1431 3.205507 AGGAGAGTGAGGTAGCATAAGGA 59.794 47.826 0.00 0.00 0.00 3.36
1070 1436 3.107402 TGAAGGAGAGTGAGGTAGCAT 57.893 47.619 0.00 0.00 0.00 3.79
1104 1470 2.134287 GCAGTAGGAGCCGGGATCA 61.134 63.158 15.10 0.00 0.00 2.92
1590 1956 1.067060 CTGATCTCCGCGGTCATTGTA 59.933 52.381 27.15 1.93 0.00 2.41
2184 2556 5.397672 CCTCCCTTGAACAGATGATTCAGAT 60.398 44.000 0.00 0.00 37.38 2.90
2357 2729 2.023788 GCCATTTTAGCAGCCTGCCTA 61.024 52.381 14.25 2.35 46.52 3.93
2575 2948 7.966812 ACTTGACAGTAGCATTGATATGGATA 58.033 34.615 0.00 0.00 32.15 2.59
2663 3091 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2667 3095 6.293955 CGTTTGTGGTAGTCCATTTGAAATCT 60.294 38.462 0.00 0.00 46.20 2.40
2668 3096 5.856455 CGTTTGTGGTAGTCCATTTGAAATC 59.144 40.000 0.00 0.00 46.20 2.17
2683 3111 6.474140 TGTCTATATACATCCGTTTGTGGT 57.526 37.500 0.00 0.00 0.00 4.16
2684 3112 9.653287 AATATGTCTATATACATCCGTTTGTGG 57.347 33.333 7.00 0.00 40.52 4.17
2725 3155 3.625764 GGCTACATACGGAGCAAAATGAA 59.374 43.478 0.00 0.00 40.64 2.57
2733 3163 1.134788 ACAAGTGGCTACATACGGAGC 60.135 52.381 2.02 0.00 38.00 4.70
2735 3165 2.563620 TCAACAAGTGGCTACATACGGA 59.436 45.455 2.02 0.00 0.00 4.69
2746 3176 7.442364 TGTCTTTCTAGAGATTTCAACAAGTGG 59.558 37.037 0.00 0.00 0.00 4.00
2774 3204 9.453830 AGAACTACTCCCTCCATTCTTAAATAT 57.546 33.333 0.00 0.00 0.00 1.28
2781 3211 5.804771 GCAAAAGAACTACTCCCTCCATTCT 60.805 44.000 0.00 0.00 0.00 2.40
2785 3215 2.979678 AGCAAAAGAACTACTCCCTCCA 59.020 45.455 0.00 0.00 0.00 3.86
2795 3225 2.106511 TGAGGGCTACAGCAAAAGAACT 59.893 45.455 3.24 0.00 44.36 3.01
2796 3226 2.485814 CTGAGGGCTACAGCAAAAGAAC 59.514 50.000 3.24 0.00 44.36 3.01
2797 3227 2.783135 CTGAGGGCTACAGCAAAAGAA 58.217 47.619 3.24 0.00 44.36 2.52
2798 3228 2.479566 CTGAGGGCTACAGCAAAAGA 57.520 50.000 3.24 0.00 44.36 2.52
2805 3235 1.117994 TCTGATGCTGAGGGCTACAG 58.882 55.000 7.00 7.00 41.72 2.74
2806 3236 1.798626 ATCTGATGCTGAGGGCTACA 58.201 50.000 0.00 0.00 42.39 2.74
2807 3237 2.926778 AATCTGATGCTGAGGGCTAC 57.073 50.000 0.00 0.00 42.39 3.58
2808 3238 4.842948 AGAATAATCTGATGCTGAGGGCTA 59.157 41.667 0.00 0.00 36.79 3.93
2809 3239 3.651904 AGAATAATCTGATGCTGAGGGCT 59.348 43.478 0.00 0.00 36.79 5.19
2810 3240 4.018484 AGAATAATCTGATGCTGAGGGC 57.982 45.455 0.00 0.00 36.54 5.19
2892 3322 0.783850 ATTGTGGTTGGCCCTAGGTT 59.216 50.000 8.29 0.00 0.00 3.50
2894 3324 1.937191 AAATTGTGGTTGGCCCTAGG 58.063 50.000 0.06 0.06 0.00 3.02
2896 3326 1.889829 CGAAAATTGTGGTTGGCCCTA 59.110 47.619 0.00 0.00 0.00 3.53
2898 3328 0.391228 ACGAAAATTGTGGTTGGCCC 59.609 50.000 0.00 0.00 0.00 5.80
2899 3329 1.604438 GGACGAAAATTGTGGTTGGCC 60.604 52.381 0.00 0.00 0.00 5.36
2906 3337 3.502211 ACTAGCTTGGGACGAAAATTGTG 59.498 43.478 0.00 0.00 0.00 3.33
2955 3391 3.754965 TCTCTTTTGGGTTCTCACATGG 58.245 45.455 0.00 0.00 0.00 3.66
3107 3543 8.788325 AGAGTAATTGTTGGTAATGGACTAAC 57.212 34.615 0.00 0.00 46.78 2.34
3142 3578 7.552687 GTCAAATGTAACATCAGGGAAGACATA 59.447 37.037 0.00 0.00 0.00 2.29
3143 3579 6.375455 GTCAAATGTAACATCAGGGAAGACAT 59.625 38.462 0.00 0.00 0.00 3.06
3163 3601 8.359875 TCATCATAATAAAAAGGCCAGTCAAA 57.640 30.769 5.01 0.00 0.00 2.69
3171 3609 6.731292 ACCCCTTCATCATAATAAAAAGGC 57.269 37.500 0.00 0.00 33.48 4.35
3182 3620 5.605540 AAGCCAATATACCCCTTCATCAT 57.394 39.130 0.00 0.00 0.00 2.45
3183 3621 6.718593 ATAAGCCAATATACCCCTTCATCA 57.281 37.500 0.00 0.00 0.00 3.07
3184 3622 8.422577 AAAATAAGCCAATATACCCCTTCATC 57.577 34.615 0.00 0.00 0.00 2.92
3266 3704 5.772393 TGTACCTGTCAATGGAAGGTTAT 57.228 39.130 11.89 0.00 41.65 1.89
3267 3705 5.570205 TTGTACCTGTCAATGGAAGGTTA 57.430 39.130 11.89 1.95 41.65 2.85
3268 3706 4.447138 TTGTACCTGTCAATGGAAGGTT 57.553 40.909 11.89 0.00 41.65 3.50
3302 3743 3.819920 CGCAGAGCAGAGCCGAGA 61.820 66.667 0.00 0.00 0.00 4.04
3323 3764 0.179936 GCTCCCACTCTGAATGGAGG 59.820 60.000 6.74 0.11 43.74 4.30
3359 3800 1.689984 TGTTGCTTGGCTTGATGTCA 58.310 45.000 0.00 0.00 0.00 3.58
3506 3947 0.878523 TCGGCCTTCTTGTGTTGACG 60.879 55.000 0.00 0.00 0.00 4.35
3773 4214 2.584608 GCCTGTGCCATAGACGGT 59.415 61.111 0.00 0.00 0.00 4.83
4251 4701 8.245195 TGGGCTTAATAAGATTATTTCAACCC 57.755 34.615 3.88 9.57 35.20 4.11
4264 4714 9.199982 CAAGCATATGAAATTGGGCTTAATAAG 57.800 33.333 6.97 0.00 39.36 1.73
4391 4841 7.339466 AGTTATCAGTTTTCGCAGGGATTATTT 59.661 33.333 0.00 0.00 0.00 1.40
4403 4853 8.918961 ACAGATCTAAGAGTTATCAGTTTTCG 57.081 34.615 0.00 0.00 0.00 3.46
4445 4895 1.303309 AGATGGCGTTGATGCTAAGC 58.697 50.000 0.00 0.00 34.52 3.09
4451 4901 8.773645 TCACTTATAATAAAGATGGCGTTGATG 58.226 33.333 0.00 0.00 0.00 3.07
4454 4904 8.365399 TCTCACTTATAATAAAGATGGCGTTG 57.635 34.615 0.00 0.00 0.00 4.10
4474 4924 3.057734 ACAACCGAAACGATTCTCTCAC 58.942 45.455 3.81 0.00 33.17 3.51
4484 4934 2.540516 TGTACATCACACAACCGAAACG 59.459 45.455 0.00 0.00 30.04 3.60
4510 4960 0.467474 TCATATCTGACCCTCGCCGT 60.467 55.000 0.00 0.00 0.00 5.68
4529 4979 2.576648 GGAAGGGAGAAAGGGTATGTGT 59.423 50.000 0.00 0.00 0.00 3.72
4543 4993 2.657459 AGAGAGAAAGAGAGGGAAGGGA 59.343 50.000 0.00 0.00 0.00 4.20
4573 5023 0.110486 ACTGATTTGTGGGCTCCGTT 59.890 50.000 0.00 0.00 0.00 4.44
4596 5046 1.271543 TGGCAATGGTGAGAGGTCAAG 60.272 52.381 0.00 0.00 33.27 3.02
4643 5094 3.001406 AGGGACGGTAGCACCACC 61.001 66.667 7.31 7.66 38.47 4.61
4654 5105 1.075970 TCAGGGATGGAGAGGGACG 60.076 63.158 0.00 0.00 0.00 4.79
4655 5106 1.406860 GCTCAGGGATGGAGAGGGAC 61.407 65.000 0.00 0.00 34.24 4.46
4670 5121 2.747686 GAAAGGTCCACGGGCTCA 59.252 61.111 0.00 0.00 0.00 4.26
4683 5134 0.961753 GAGGGTTTGCACCTGGAAAG 59.038 55.000 0.00 0.00 43.65 2.62
4685 5136 0.467290 GTGAGGGTTTGCACCTGGAA 60.467 55.000 0.00 0.00 43.65 3.53
4709 5160 2.340443 GATAAGGAGAGGCCGCGG 59.660 66.667 24.05 24.05 43.43 6.46
4710 5161 2.049985 CGATAAGGAGAGGCCGCG 60.050 66.667 0.00 0.00 43.43 6.46
4714 5165 2.614520 GCCTTTTTCGATAAGGAGAGGC 59.385 50.000 23.75 17.86 44.01 4.70
4735 5186 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
4736 5187 5.823353 CTTTATTTATAAAGCGGGGCGAAA 58.177 37.500 8.78 0.00 41.69 3.46
4737 5188 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
4747 5198 8.580720 TCTGTGGCAGTTTGCTTTATTTATAAA 58.419 29.630 0.00 0.00 44.28 1.40
4748 5199 8.116651 TCTGTGGCAGTTTGCTTTATTTATAA 57.883 30.769 0.67 0.00 44.28 0.98
4749 5200 7.628366 GCTCTGTGGCAGTTTGCTTTATTTATA 60.628 37.037 0.67 0.00 44.28 0.98
4750 5201 6.588719 TCTGTGGCAGTTTGCTTTATTTAT 57.411 33.333 0.67 0.00 44.28 1.40
4751 5202 5.564651 GCTCTGTGGCAGTTTGCTTTATTTA 60.565 40.000 0.67 0.00 44.28 1.40
4752 5203 4.797275 GCTCTGTGGCAGTTTGCTTTATTT 60.797 41.667 0.67 0.00 44.28 1.40
4753 5204 3.305608 GCTCTGTGGCAGTTTGCTTTATT 60.306 43.478 0.67 0.00 44.28 1.40
4754 5205 2.229784 GCTCTGTGGCAGTTTGCTTTAT 59.770 45.455 0.67 0.00 44.28 1.40
4755 5206 1.608590 GCTCTGTGGCAGTTTGCTTTA 59.391 47.619 0.67 0.00 44.28 1.85
4756 5207 0.386838 GCTCTGTGGCAGTTTGCTTT 59.613 50.000 0.67 0.00 44.28 3.51
4757 5208 0.752743 TGCTCTGTGGCAGTTTGCTT 60.753 50.000 0.67 0.00 44.28 3.91
4758 5209 0.752743 TTGCTCTGTGGCAGTTTGCT 60.753 50.000 0.67 0.00 44.28 3.91
4759 5210 0.595825 GTTGCTCTGTGGCAGTTTGC 60.596 55.000 0.00 0.00 43.39 3.68
4760 5211 0.031178 GGTTGCTCTGTGGCAGTTTG 59.969 55.000 0.00 0.00 43.39 2.93
4761 5212 0.395586 TGGTTGCTCTGTGGCAGTTT 60.396 50.000 0.00 0.00 43.39 2.66
4762 5213 0.178981 ATGGTTGCTCTGTGGCAGTT 60.179 50.000 0.00 0.00 43.39 3.16
4763 5214 0.692476 TATGGTTGCTCTGTGGCAGT 59.308 50.000 0.00 0.00 43.39 4.40
4764 5215 1.089920 GTATGGTTGCTCTGTGGCAG 58.910 55.000 0.00 0.00 43.39 4.85
4765 5216 0.399833 TGTATGGTTGCTCTGTGGCA 59.600 50.000 0.00 0.00 40.74 4.92
4766 5217 1.470098 CTTGTATGGTTGCTCTGTGGC 59.530 52.381 0.00 0.00 0.00 5.01
4767 5218 2.086869 CCTTGTATGGTTGCTCTGTGG 58.913 52.381 0.00 0.00 0.00 4.17
4768 5219 2.744202 GTCCTTGTATGGTTGCTCTGTG 59.256 50.000 0.00 0.00 0.00 3.66
4769 5220 2.639839 AGTCCTTGTATGGTTGCTCTGT 59.360 45.455 0.00 0.00 0.00 3.41
4770 5221 3.340814 AGTCCTTGTATGGTTGCTCTG 57.659 47.619 0.00 0.00 0.00 3.35
4771 5222 4.097418 ACTAGTCCTTGTATGGTTGCTCT 58.903 43.478 0.00 0.00 0.00 4.09
4772 5223 4.434520 GACTAGTCCTTGTATGGTTGCTC 58.565 47.826 12.13 0.00 0.00 4.26
4773 5224 3.197983 GGACTAGTCCTTGTATGGTTGCT 59.802 47.826 31.12 0.00 46.16 3.91
4774 5225 3.532542 GGACTAGTCCTTGTATGGTTGC 58.467 50.000 31.12 3.12 46.16 4.17
4787 5238 3.381949 GTGTGTGAGTTGTGGACTAGTC 58.618 50.000 14.87 14.87 39.19 2.59
4788 5239 2.102588 GGTGTGTGAGTTGTGGACTAGT 59.897 50.000 0.00 0.00 39.19 2.57
4789 5240 2.548067 GGGTGTGTGAGTTGTGGACTAG 60.548 54.545 0.00 0.00 39.19 2.57
4790 5241 1.414919 GGGTGTGTGAGTTGTGGACTA 59.585 52.381 0.00 0.00 39.19 2.59
4791 5242 0.180406 GGGTGTGTGAGTTGTGGACT 59.820 55.000 0.00 0.00 42.70 3.85
4792 5243 0.107410 TGGGTGTGTGAGTTGTGGAC 60.107 55.000 0.00 0.00 0.00 4.02
4793 5244 0.107410 GTGGGTGTGTGAGTTGTGGA 60.107 55.000 0.00 0.00 0.00 4.02
4794 5245 1.436195 CGTGGGTGTGTGAGTTGTGG 61.436 60.000 0.00 0.00 0.00 4.17
4795 5246 0.742990 ACGTGGGTGTGTGAGTTGTG 60.743 55.000 0.00 0.00 0.00 3.33
4796 5247 0.461339 GACGTGGGTGTGTGAGTTGT 60.461 55.000 0.00 0.00 0.00 3.32
4797 5248 0.179084 AGACGTGGGTGTGTGAGTTG 60.179 55.000 0.00 0.00 0.00 3.16
4798 5249 0.104304 GAGACGTGGGTGTGTGAGTT 59.896 55.000 0.00 0.00 0.00 3.01
4799 5250 1.040893 TGAGACGTGGGTGTGTGAGT 61.041 55.000 0.00 0.00 0.00 3.41
4800 5251 0.597637 GTGAGACGTGGGTGTGTGAG 60.598 60.000 0.00 0.00 0.00 3.51
4801 5252 1.440060 GTGAGACGTGGGTGTGTGA 59.560 57.895 0.00 0.00 0.00 3.58
4802 5253 1.949133 CGTGAGACGTGGGTGTGTG 60.949 63.158 0.00 0.00 36.74 3.82
4803 5254 2.122797 TCGTGAGACGTGGGTGTGT 61.123 57.895 0.00 0.00 43.14 3.72
4804 5255 2.725641 TCGTGAGACGTGGGTGTG 59.274 61.111 0.00 0.00 43.14 3.82
4814 5265 6.518493 ACCTTTTGTACTTATTGTCGTGAGA 58.482 36.000 0.00 0.00 38.16 3.27
4815 5266 6.780706 ACCTTTTGTACTTATTGTCGTGAG 57.219 37.500 0.00 0.00 0.00 3.51
4816 5267 6.987992 AGAACCTTTTGTACTTATTGTCGTGA 59.012 34.615 0.00 0.00 0.00 4.35
4817 5268 7.069569 CAGAACCTTTTGTACTTATTGTCGTG 58.930 38.462 0.00 0.00 0.00 4.35
4818 5269 6.764560 ACAGAACCTTTTGTACTTATTGTCGT 59.235 34.615 0.00 0.00 0.00 4.34
4819 5270 7.186021 ACAGAACCTTTTGTACTTATTGTCG 57.814 36.000 0.00 0.00 0.00 4.35
4820 5271 8.617809 TCAACAGAACCTTTTGTACTTATTGTC 58.382 33.333 0.00 0.00 0.00 3.18
4821 5272 8.514330 TCAACAGAACCTTTTGTACTTATTGT 57.486 30.769 0.00 0.00 0.00 2.71
4822 5273 8.076178 CCTCAACAGAACCTTTTGTACTTATTG 58.924 37.037 0.00 0.00 0.00 1.90
4823 5274 7.230712 CCCTCAACAGAACCTTTTGTACTTATT 59.769 37.037 0.00 0.00 0.00 1.40
4824 5275 6.715264 CCCTCAACAGAACCTTTTGTACTTAT 59.285 38.462 0.00 0.00 0.00 1.73
4825 5276 6.059484 CCCTCAACAGAACCTTTTGTACTTA 58.941 40.000 0.00 0.00 0.00 2.24
4826 5277 4.887655 CCCTCAACAGAACCTTTTGTACTT 59.112 41.667 0.00 0.00 0.00 2.24
4827 5278 4.461198 CCCTCAACAGAACCTTTTGTACT 58.539 43.478 0.00 0.00 0.00 2.73
4828 5279 3.004419 GCCCTCAACAGAACCTTTTGTAC 59.996 47.826 0.00 0.00 0.00 2.90
4829 5280 3.219281 GCCCTCAACAGAACCTTTTGTA 58.781 45.455 0.00 0.00 0.00 2.41
4830 5281 2.031870 GCCCTCAACAGAACCTTTTGT 58.968 47.619 0.00 0.00 0.00 2.83
4831 5282 2.031120 TGCCCTCAACAGAACCTTTTG 58.969 47.619 0.00 0.00 0.00 2.44
4832 5283 2.031870 GTGCCCTCAACAGAACCTTTT 58.968 47.619 0.00 0.00 0.00 2.27
4833 5284 1.064017 TGTGCCCTCAACAGAACCTTT 60.064 47.619 0.00 0.00 0.00 3.11
4834 5285 0.550914 TGTGCCCTCAACAGAACCTT 59.449 50.000 0.00 0.00 0.00 3.50
4835 5286 0.109342 CTGTGCCCTCAACAGAACCT 59.891 55.000 0.00 0.00 33.65 3.50
4836 5287 1.518903 GCTGTGCCCTCAACAGAACC 61.519 60.000 7.72 0.00 33.65 3.62
4837 5288 0.536006 AGCTGTGCCCTCAACAGAAC 60.536 55.000 7.72 0.00 33.65 3.01
4838 5289 0.250467 GAGCTGTGCCCTCAACAGAA 60.250 55.000 7.72 0.00 33.65 3.02
4839 5290 1.372683 GAGCTGTGCCCTCAACAGA 59.627 57.895 7.72 0.00 33.65 3.41
4840 5291 0.535780 TTGAGCTGTGCCCTCAACAG 60.536 55.000 0.00 0.00 42.58 3.16
4841 5292 1.531259 TTGAGCTGTGCCCTCAACA 59.469 52.632 0.00 0.00 42.58 3.33
4842 5293 4.481195 TTGAGCTGTGCCCTCAAC 57.519 55.556 0.00 0.00 42.58 3.18
4843 5294 0.106769 TTGTTGAGCTGTGCCCTCAA 60.107 50.000 0.00 0.09 44.54 3.02
4844 5295 0.535780 CTTGTTGAGCTGTGCCCTCA 60.536 55.000 0.00 0.00 37.54 3.86
4845 5296 2.251600 CTTGTTGAGCTGTGCCCTC 58.748 57.895 0.00 0.00 0.00 4.30
4846 5297 4.488790 CTTGTTGAGCTGTGCCCT 57.511 55.556 0.00 0.00 0.00 5.19
4855 5306 4.122143 TCTTTTGTTTGGGCTTGTTGAG 57.878 40.909 0.00 0.00 0.00 3.02
4856 5307 4.543590 TTCTTTTGTTTGGGCTTGTTGA 57.456 36.364 0.00 0.00 0.00 3.18
4857 5308 5.619625 TTTTCTTTTGTTTGGGCTTGTTG 57.380 34.783 0.00 0.00 0.00 3.33
4858 5309 6.000840 TCTTTTTCTTTTGTTTGGGCTTGTT 58.999 32.000 0.00 0.00 0.00 2.83
4859 5310 5.555966 TCTTTTTCTTTTGTTTGGGCTTGT 58.444 33.333 0.00 0.00 0.00 3.16
4860 5311 6.493449 TTCTTTTTCTTTTGTTTGGGCTTG 57.507 33.333 0.00 0.00 0.00 4.01
4861 5312 6.095300 CCATTCTTTTTCTTTTGTTTGGGCTT 59.905 34.615 0.00 0.00 0.00 4.35
4862 5313 5.589855 CCATTCTTTTTCTTTTGTTTGGGCT 59.410 36.000 0.00 0.00 0.00 5.19
4863 5314 5.733091 GCCATTCTTTTTCTTTTGTTTGGGC 60.733 40.000 0.00 0.00 0.00 5.36
4864 5315 5.221028 GGCCATTCTTTTTCTTTTGTTTGGG 60.221 40.000 0.00 0.00 0.00 4.12
4865 5316 5.503846 CGGCCATTCTTTTTCTTTTGTTTGG 60.504 40.000 2.24 0.00 0.00 3.28
4866 5317 5.500825 CGGCCATTCTTTTTCTTTTGTTTG 58.499 37.500 2.24 0.00 0.00 2.93
4867 5318 4.574421 CCGGCCATTCTTTTTCTTTTGTTT 59.426 37.500 2.24 0.00 0.00 2.83
4868 5319 4.126437 CCGGCCATTCTTTTTCTTTTGTT 58.874 39.130 2.24 0.00 0.00 2.83
4869 5320 3.494223 CCCGGCCATTCTTTTTCTTTTGT 60.494 43.478 2.24 0.00 0.00 2.83
4870 5321 3.066380 CCCGGCCATTCTTTTTCTTTTG 58.934 45.455 2.24 0.00 0.00 2.44
4871 5322 2.038426 CCCCGGCCATTCTTTTTCTTTT 59.962 45.455 2.24 0.00 0.00 2.27
4872 5323 1.623311 CCCCGGCCATTCTTTTTCTTT 59.377 47.619 2.24 0.00 0.00 2.52
4873 5324 1.266178 CCCCGGCCATTCTTTTTCTT 58.734 50.000 2.24 0.00 0.00 2.52
4874 5325 0.614697 CCCCCGGCCATTCTTTTTCT 60.615 55.000 2.24 0.00 0.00 2.52
4875 5326 0.613572 TCCCCCGGCCATTCTTTTTC 60.614 55.000 2.24 0.00 0.00 2.29
4876 5327 0.614697 CTCCCCCGGCCATTCTTTTT 60.615 55.000 2.24 0.00 0.00 1.94
4877 5328 1.000359 CTCCCCCGGCCATTCTTTT 60.000 57.895 2.24 0.00 0.00 2.27
4878 5329 2.683475 CTCCCCCGGCCATTCTTT 59.317 61.111 2.24 0.00 0.00 2.52
4879 5330 3.420482 CCTCCCCCGGCCATTCTT 61.420 66.667 2.24 0.00 0.00 2.52
4905 5356 4.963428 GATTAGGGGTCGGGCGCG 62.963 72.222 18.21 18.21 0.00 6.86
4906 5357 4.620937 GGATTAGGGGTCGGGCGC 62.621 72.222 0.00 0.00 0.00 6.53
4907 5358 4.295119 CGGATTAGGGGTCGGGCG 62.295 72.222 0.00 0.00 0.00 6.13
4908 5359 3.937447 CCGGATTAGGGGTCGGGC 61.937 72.222 0.00 0.00 38.93 6.13
4909 5360 3.937447 GCCGGATTAGGGGTCGGG 61.937 72.222 5.05 0.00 42.43 5.14
4910 5361 2.842936 AGCCGGATTAGGGGTCGG 60.843 66.667 5.05 0.00 44.70 4.79
4911 5362 2.735237 GAGCCGGATTAGGGGTCG 59.265 66.667 5.05 0.00 41.66 4.79
4912 5363 2.735237 CGAGCCGGATTAGGGGTC 59.265 66.667 5.05 0.11 46.13 4.46


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

AutoCloner maintained by Alex Coulton.