Multiple sequence alignment - TraesCS3D01G087300

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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 TraesCS3D01G087300 chr3D 100.000 5259 0 0 1 5259 44012111 44006853 0.000000e+00 9712.0
1 TraesCS3D01G087300 chr3D 95.455 110 5 0 4675 4784 68912241 68912132 5.410000e-40 176.0
2 TraesCS3D01G087300 chr3D 92.562 121 8 1 4675 4795 260294089 260294208 7.000000e-39 172.0
3 TraesCS3D01G087300 chr3A 92.139 3829 195 50 909 4679 56230257 56226477 0.000000e+00 5306.0
4 TraesCS3D01G087300 chr3A 84.692 908 90 23 3 877 56231447 56230556 0.000000e+00 861.0
5 TraesCS3D01G087300 chr3A 86.093 302 23 10 4864 5149 56226406 56226108 1.840000e-79 307.0
6 TraesCS3D01G087300 chr3B 95.150 1567 57 9 1908 3473 68913453 68911905 0.000000e+00 2455.0
7 TraesCS3D01G087300 chr3B 90.964 1162 65 16 683 1822 68914819 68913676 0.000000e+00 1528.0
8 TraesCS3D01G087300 chr3B 89.207 1047 71 23 3664 4679 68911901 68910866 0.000000e+00 1269.0
9 TraesCS3D01G087300 chr3B 87.482 703 62 14 3 685 68915574 68914878 0.000000e+00 787.0
10 TraesCS3D01G087300 chr3B 88.715 576 43 10 3 560 68922242 68921671 0.000000e+00 684.0
11 TraesCS3D01G087300 chr3B 83.826 507 27 18 4783 5255 68910867 68910382 1.050000e-116 431.0
12 TraesCS3D01G087300 chr3B 93.662 142 8 1 3583 3723 406542354 406542495 1.480000e-50 211.0
13 TraesCS3D01G087300 chr4D 94.444 144 7 1 3581 3723 303078577 303078434 2.470000e-53 220.0
14 TraesCS3D01G087300 chr4D 92.517 147 7 1 3581 3723 65943614 65943760 1.920000e-49 207.0
15 TraesCS3D01G087300 chr1B 93.662 142 8 1 3581 3721 229239556 229239697 1.480000e-50 211.0
16 TraesCS3D01G087300 chr2D 92.361 144 10 1 3581 3723 277939921 277940064 2.480000e-48 204.0
17 TraesCS3D01G087300 chr2D 90.476 126 10 2 4662 4786 608980215 608980339 1.170000e-36 165.0
18 TraesCS3D01G087300 chr2D 100.000 35 0 0 694 728 429492456 429492422 1.220000e-06 65.8
19 TraesCS3D01G087300 chr5D 92.308 143 9 1 3581 3723 152753324 152753464 8.930000e-48 202.0
20 TraesCS3D01G087300 chr5D 95.536 112 4 1 4675 4786 68696994 68696884 1.500000e-40 178.0
21 TraesCS3D01G087300 chr5D 96.262 107 4 0 4675 4781 365693304 365693410 5.410000e-40 176.0
22 TraesCS3D01G087300 chr2A 92.308 143 9 1 3581 3723 144847531 144847671 8.930000e-48 202.0
23 TraesCS3D01G087300 chr1D 91.837 147 8 1 3581 3723 194673729 194673875 8.930000e-48 202.0
24 TraesCS3D01G087300 chr7B 97.196 107 3 0 4675 4781 683101467 683101573 1.160000e-41 182.0
25 TraesCS3D01G087300 chr5A 96.262 107 4 0 4675 4781 467377453 467377559 5.410000e-40 176.0
26 TraesCS3D01G087300 chr2B 92.562 121 9 0 4675 4795 663123649 663123529 1.950000e-39 174.0
27 TraesCS3D01G087300 chr4B 93.860 114 7 0 4668 4781 414860859 414860746 7.000000e-39 172.0


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 TraesCS3D01G087300 chr3D 44006853 44012111 5258 True 9712 9712 100.000000 1 5259 1 chr3D.!!$R1 5258
1 TraesCS3D01G087300 chr3A 56226108 56231447 5339 True 2158 5306 87.641333 3 5149 3 chr3A.!!$R1 5146
2 TraesCS3D01G087300 chr3B 68910382 68915574 5192 True 1294 2455 89.325800 3 5255 5 chr3B.!!$R2 5252
3 TraesCS3D01G087300 chr3B 68921671 68922242 571 True 684 684 88.715000 3 560 1 chr3B.!!$R1 557

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
926 1312 1.005569 CATCCATCCATCCATCCCCTG 59.994 57.143 0.0 0.0 0.00 4.45 F
1366 1763 0.539518 TACTGATGCCGCAAAGCCTA 59.460 50.000 0.0 0.0 0.00 3.93 F
1512 1912 1.200020 GCACCCGTCTCAGGATTTTTG 59.800 52.381 0.0 0.0 0.00 2.44 F
2111 2671 1.202568 CGCTGAACTTGTGCTCACG 59.797 57.895 0.0 0.0 0.00 4.35 F
3688 4255 0.039911 ACTAGGCACGAGGAGGAGTT 59.960 55.000 0.0 0.0 34.62 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2677 0.532115 CCCCTTTCATCCCTTTTGCG 59.468 55.000 0.00 0.0 0.00 4.85 R
3357 3924 1.211457 GTGAGTCATGATTCCCCTGCT 59.789 52.381 14.93 0.0 0.00 4.24 R
3474 4041 1.026718 GGCTCAAACACGCTGCCTAT 61.027 55.000 0.00 0.0 40.36 2.57 R
3763 4346 0.544595 GTGGTCTCCTACACCCTGGT 60.545 60.000 0.00 0.0 32.24 4.00 R
5119 5772 0.903236 GGGTAGGGTTCTCTGTGTCC 59.097 60.000 0.00 0.0 0.00 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.652727 AGCTCTCTAAATCAAACCAAAAGTTC 58.347 34.615 0.00 0.00 37.88 3.01
26 27 7.285401 AGCTCTCTAAATCAAACCAAAAGTTCA 59.715 33.333 0.00 0.00 37.88 3.18
144 149 9.125026 GATGAAATGTAACCCATAGTTCATTCT 57.875 33.333 0.00 0.00 39.46 2.40
185 213 4.989168 ACCACGTTTAAAAAGCAACAACAA 59.011 33.333 0.00 0.00 0.00 2.83
248 276 1.069906 GCACCAACAATCTCGACACAC 60.070 52.381 0.00 0.00 0.00 3.82
251 279 2.034939 ACCAACAATCTCGACACACGTA 59.965 45.455 0.00 0.00 43.13 3.57
371 407 8.682936 ACACATGGATCCTATTAATTGAGAAC 57.317 34.615 14.23 0.00 0.00 3.01
393 429 7.671398 AGAACCATACACATTCCTCAAGAAAAT 59.329 33.333 0.00 0.00 38.21 1.82
490 536 3.010624 TCCATTGTTGCACATGAAACG 57.989 42.857 0.00 0.00 36.34 3.60
498 544 2.088423 TGCACATGAAACGAATACCCC 58.912 47.619 0.00 0.00 0.00 4.95
507 553 4.021192 TGAAACGAATACCCCGTACTCTTT 60.021 41.667 0.00 0.00 39.57 2.52
524 570 9.340695 CGTACTCTTTTGATGAAATTTTGCATA 57.659 29.630 0.00 0.00 0.00 3.14
622 669 1.750778 CGCCATTCAAAACCAGGCTAT 59.249 47.619 0.00 0.00 43.07 2.97
660 708 6.815142 ACGGTTTTATGAATTCTAGTAGCGTT 59.185 34.615 7.05 0.00 34.12 4.84
687 797 1.686052 GAATGCCCACACTTCAAACCA 59.314 47.619 0.00 0.00 0.00 3.67
713 823 2.262915 CCGTGTCTCAGTCCCAGC 59.737 66.667 0.00 0.00 0.00 4.85
728 838 2.507944 AGCGTGGCTGATCATCCC 59.492 61.111 12.97 9.09 37.57 3.85
844 957 6.035650 CGATGAACGAATGTACTAACACCATT 59.964 38.462 0.00 0.00 45.77 3.16
866 979 2.632996 TCCAGGTCCGAATACATCCATC 59.367 50.000 0.00 0.00 0.00 3.51
867 980 2.289694 CCAGGTCCGAATACATCCATCC 60.290 54.545 0.00 0.00 0.00 3.51
868 981 2.368548 CAGGTCCGAATACATCCATCCA 59.631 50.000 0.00 0.00 0.00 3.41
869 982 3.045634 AGGTCCGAATACATCCATCCAA 58.954 45.455 0.00 0.00 0.00 3.53
908 1021 2.555664 AGAGGCCCATATTCGATCCAT 58.444 47.619 0.00 0.00 0.00 3.41
910 1023 1.561542 AGGCCCATATTCGATCCATCC 59.438 52.381 0.00 0.00 0.00 3.51
912 1025 2.092212 GGCCCATATTCGATCCATCCAT 60.092 50.000 0.00 0.00 0.00 3.41
913 1026 3.209410 GCCCATATTCGATCCATCCATC 58.791 50.000 0.00 0.00 0.00 3.51
914 1027 3.813443 CCCATATTCGATCCATCCATCC 58.187 50.000 0.00 0.00 0.00 3.51
915 1028 3.200605 CCCATATTCGATCCATCCATCCA 59.799 47.826 0.00 0.00 0.00 3.41
926 1312 1.005569 CATCCATCCATCCATCCCCTG 59.994 57.143 0.00 0.00 0.00 4.45
1259 1650 1.619827 CCAGGTAACCAACACCGTCTA 59.380 52.381 0.00 0.00 41.21 2.59
1293 1684 2.749621 AGTTCAATCGCTCCATTTCCAC 59.250 45.455 0.00 0.00 0.00 4.02
1295 1686 2.632377 TCAATCGCTCCATTTCCACTC 58.368 47.619 0.00 0.00 0.00 3.51
1297 1688 2.611225 ATCGCTCCATTTCCACTCTC 57.389 50.000 0.00 0.00 0.00 3.20
1306 1697 1.140312 TTTCCACTCTCTGCCCAGTT 58.860 50.000 0.00 0.00 0.00 3.16
1315 1706 2.312140 TCTCTGCCCAGTTAGGAGTAGT 59.688 50.000 0.00 0.00 41.22 2.73
1334 1725 1.562475 GTGGGGTTGGTAGGATTGCTA 59.438 52.381 0.00 0.00 0.00 3.49
1335 1726 1.843851 TGGGGTTGGTAGGATTGCTAG 59.156 52.381 0.00 0.00 0.00 3.42
1357 1754 1.683917 ACCTAGAGCTTACTGATGCCG 59.316 52.381 0.00 0.00 0.00 5.69
1366 1763 0.539518 TACTGATGCCGCAAAGCCTA 59.460 50.000 0.00 0.00 0.00 3.93
1441 1838 5.887598 TCAAATCATCCTAGTTTCACATGGG 59.112 40.000 0.00 0.00 0.00 4.00
1457 1854 4.628333 CACATGGGCAAATTCTTTAGCAAG 59.372 41.667 0.00 0.00 0.00 4.01
1474 1874 8.939201 TTTAGCAAGAAAACAAAACATCATCA 57.061 26.923 0.00 0.00 0.00 3.07
1475 1875 9.545105 TTTAGCAAGAAAACAAAACATCATCAT 57.455 25.926 0.00 0.00 0.00 2.45
1476 1876 7.647907 AGCAAGAAAACAAAACATCATCATC 57.352 32.000 0.00 0.00 0.00 2.92
1477 1877 7.211573 AGCAAGAAAACAAAACATCATCATCA 58.788 30.769 0.00 0.00 0.00 3.07
1478 1878 7.384115 AGCAAGAAAACAAAACATCATCATCAG 59.616 33.333 0.00 0.00 0.00 2.90
1484 1884 7.698506 AACAAAACATCATCATCAGTCTCAT 57.301 32.000 0.00 0.00 0.00 2.90
1488 1888 9.880064 CAAAACATCATCATCAGTCTCATAATC 57.120 33.333 0.00 0.00 0.00 1.75
1512 1912 1.200020 GCACCCGTCTCAGGATTTTTG 59.800 52.381 0.00 0.00 0.00 2.44
1517 1917 3.317993 CCCGTCTCAGGATTTTTGTTGTT 59.682 43.478 0.00 0.00 0.00 2.83
1518 1918 4.290155 CCGTCTCAGGATTTTTGTTGTTG 58.710 43.478 0.00 0.00 0.00 3.33
1519 1919 4.202010 CCGTCTCAGGATTTTTGTTGTTGT 60.202 41.667 0.00 0.00 0.00 3.32
1520 1920 5.339990 CGTCTCAGGATTTTTGTTGTTGTT 58.660 37.500 0.00 0.00 0.00 2.83
1521 1921 5.229887 CGTCTCAGGATTTTTGTTGTTGTTG 59.770 40.000 0.00 0.00 0.00 3.33
1597 1997 2.434884 ATCGTCAAGGGCTGCGTG 60.435 61.111 0.00 0.00 0.00 5.34
1636 2036 2.158696 GCTTGAGATTATGGAGCCCTGT 60.159 50.000 0.00 0.00 0.00 4.00
1690 2090 8.884124 AATTCTTATTGTCCTCCTCATTTCAA 57.116 30.769 0.00 0.00 0.00 2.69
1712 2112 2.092861 TGTTGAGGTCGTTTTCTTCCCA 60.093 45.455 0.00 0.00 0.00 4.37
1810 2210 4.993705 AGAGAAGGGTTTGATAACACCA 57.006 40.909 0.00 0.00 38.49 4.17
1874 2274 5.468072 CGCTGGCTTCTTTATCATGTTCTAT 59.532 40.000 0.00 0.00 0.00 1.98
1878 2278 6.126507 TGGCTTCTTTATCATGTTCTATCCCA 60.127 38.462 0.00 0.00 0.00 4.37
1881 2281 8.510505 GCTTCTTTATCATGTTCTATCCCATTC 58.489 37.037 0.00 0.00 0.00 2.67
1888 2288 7.206789 TCATGTTCTATCCCATTCCTAACAA 57.793 36.000 0.00 0.00 0.00 2.83
1901 2301 7.417797 CCCATTCCTAACAATTATCAACAAGGG 60.418 40.741 0.00 0.00 0.00 3.95
1911 2471 7.124147 ACAATTATCAACAAGGGAAGGGTATTG 59.876 37.037 0.00 0.00 0.00 1.90
1913 2473 2.719705 TCAACAAGGGAAGGGTATTGGT 59.280 45.455 0.00 0.00 0.00 3.67
1950 2510 9.219603 TGCATATATTAACTTATGTTCTCTGCC 57.780 33.333 0.00 0.00 37.59 4.85
1985 2545 2.365293 GGTGGAAGCAACAAGTGGAAAT 59.635 45.455 0.00 0.00 0.00 2.17
2111 2671 1.202568 CGCTGAACTTGTGCTCACG 59.797 57.895 0.00 0.00 0.00 4.35
2117 2677 1.237285 AACTTGTGCTCACGGATGCC 61.237 55.000 0.00 0.00 0.00 4.40
2159 2719 5.952947 GGCCCTAGATAAAGCTACAGAGATA 59.047 44.000 0.00 0.00 0.00 1.98
2162 2722 9.191479 GCCCTAGATAAAGCTACAGAGATATTA 57.809 37.037 0.00 0.00 0.00 0.98
2236 2796 5.627135 CCCAAAGGTAACAAGGAGAAGTAA 58.373 41.667 0.00 0.00 41.41 2.24
2238 2798 6.296803 CCAAAGGTAACAAGGAGAAGTAACT 58.703 40.000 0.00 0.00 41.41 2.24
2255 2815 9.603921 AGAAGTAACTATGTGTCTCTACTCTAC 57.396 37.037 0.00 0.00 0.00 2.59
2307 2867 7.617041 ACTTGAGGCTGATGTTTATCTTTAC 57.383 36.000 0.00 0.00 34.31 2.01
2402 2962 8.780616 ATATATTCATTGGTGGAATTGGAACA 57.219 30.769 0.00 0.00 36.45 3.18
2539 3101 8.343168 ACTCTATAGTGCTCATACTGTTATCC 57.657 38.462 0.00 0.00 33.57 2.59
2617 3179 5.028549 ACCTGGTATGTTTGCTATCAGAG 57.971 43.478 0.00 0.00 0.00 3.35
2628 3191 5.745312 TTGCTATCAGAGAAAGACTTCCA 57.255 39.130 0.00 0.00 31.28 3.53
2642 3205 7.998964 AGAAAGACTTCCATTGAGTTTTCCTTA 59.001 33.333 0.00 0.00 31.74 2.69
2694 3258 8.001881 TGTCAAACTTATGTTCTTTGCCTTAA 57.998 30.769 0.00 0.00 34.96 1.85
2699 3263 9.529325 AAACTTATGTTCTTTGCCTTAAAACTC 57.471 29.630 0.00 0.00 34.96 3.01
2932 3496 7.869016 TCACTGTATTTTCTTAACGTCTCAG 57.131 36.000 0.00 0.00 0.00 3.35
2956 3520 5.988561 GCATAGGCTGATAGGTCTATTATGC 59.011 44.000 0.00 12.16 32.54 3.14
2957 3521 6.407412 GCATAGGCTGATAGGTCTATTATGCA 60.407 42.308 17.75 0.00 40.12 3.96
2958 3522 7.688820 GCATAGGCTGATAGGTCTATTATGCAT 60.689 40.741 17.75 3.79 40.12 3.96
3040 3605 2.926200 CGTCTTCAGTCATGTGGATGTC 59.074 50.000 0.00 0.00 0.00 3.06
3072 3637 3.200825 TGAGTGGATCATCCCTCCTTTTC 59.799 47.826 15.79 0.07 34.78 2.29
3085 3650 3.054065 CCTCCTTTTCCTCTGCTTGGTAT 60.054 47.826 0.00 0.00 0.00 2.73
3140 3705 4.880164 TCTTAGGACTATTACTGCAGGGT 58.120 43.478 19.93 8.34 0.00 4.34
3274 3841 9.304731 GTATTGTAATTTCACATGTTGATGCAT 57.695 29.630 0.00 0.00 32.84 3.96
3481 4048 7.820648 AGAAATAGTGTGTTTTTGATAGGCAG 58.179 34.615 0.00 0.00 0.00 4.85
3483 4050 2.226437 AGTGTGTTTTTGATAGGCAGCG 59.774 45.455 0.00 0.00 0.00 5.18
3523 4090 6.566079 TCTGTTCATTTCTCCCATCATAGT 57.434 37.500 0.00 0.00 0.00 2.12
3528 4095 6.065976 TCATTTCTCCCATCATAGTGTTGT 57.934 37.500 0.00 0.00 0.00 3.32
3537 4104 9.342308 CTCCCATCATAGTGTTGTTAAATGTAT 57.658 33.333 0.00 0.00 0.00 2.29
3606 4173 3.134458 GAGTTGTGGAGACAGACTTTGG 58.866 50.000 0.00 0.00 44.46 3.28
3611 4178 2.996621 GTGGAGACAGACTTTGGAATCG 59.003 50.000 0.00 0.00 44.46 3.34
3655 4222 7.155328 AGAACTAAAACTGAGTACATGAGGTG 58.845 38.462 0.00 0.00 0.00 4.00
3657 4224 2.370281 AACTGAGTACATGAGGTGCG 57.630 50.000 0.00 0.00 37.18 5.34
3673 4240 3.442977 AGGTGCGGTTTCAGTACTACTAG 59.557 47.826 0.00 0.00 0.00 2.57
3687 4254 0.917533 TACTAGGCACGAGGAGGAGT 59.082 55.000 0.00 0.00 34.62 3.85
3688 4255 0.039911 ACTAGGCACGAGGAGGAGTT 59.960 55.000 0.00 0.00 34.62 3.01
3689 4256 1.284198 ACTAGGCACGAGGAGGAGTTA 59.716 52.381 0.00 0.00 34.62 2.24
3691 4258 1.142097 GGCACGAGGAGGAGTTAGC 59.858 63.158 0.00 0.00 0.00 3.09
3692 4259 1.142097 GCACGAGGAGGAGTTAGCC 59.858 63.158 0.00 0.00 0.00 3.93
3693 4260 1.324005 GCACGAGGAGGAGTTAGCCT 61.324 60.000 0.00 0.00 42.17 4.58
3866 4450 6.186957 TGTTCCTCATATGCAGTGGTTAATT 58.813 36.000 0.00 0.00 0.00 1.40
3928 4523 6.204495 CAGTCGTCTATGAATCAGAGATCAGA 59.796 42.308 10.97 8.37 34.20 3.27
3931 4526 8.081633 GTCGTCTATGAATCAGAGATCAGAAAT 58.918 37.037 10.97 0.00 34.20 2.17
4029 4624 2.202492 CAGAGACCCGAGAACGCG 60.202 66.667 3.53 3.53 38.29 6.01
4071 4666 5.961395 ATACCGCTAATCTTACAACAACG 57.039 39.130 0.00 0.00 0.00 4.10
4080 4675 8.056571 GCTAATCTTACAACAACGTGTCATATC 58.943 37.037 0.00 0.00 32.75 1.63
4100 4695 9.230122 TCATATCTCTAGCTCATAGAACTCTTG 57.770 37.037 0.00 0.00 40.06 3.02
4116 4711 5.757850 ACTCTTGTCTTGAAAACATCCAC 57.242 39.130 0.00 0.00 0.00 4.02
4117 4712 4.273480 ACTCTTGTCTTGAAAACATCCACG 59.727 41.667 0.00 0.00 0.00 4.94
4156 4751 1.537638 TGTTGTCTGTTTTGTGTGCGT 59.462 42.857 0.00 0.00 0.00 5.24
4252 4847 1.361993 CGAGAAGATGGAGGCCGAG 59.638 63.158 0.00 0.00 0.00 4.63
4307 4904 3.003793 GCTTTTTCTGCTCCGTCTTCTTT 59.996 43.478 0.00 0.00 0.00 2.52
4311 4909 1.686587 TCTGCTCCGTCTTCTTTGTCA 59.313 47.619 0.00 0.00 0.00 3.58
4394 4992 7.148755 GCTCACATTTTGTTGGTATTGATTGAC 60.149 37.037 0.00 0.00 0.00 3.18
4433 5033 5.571357 GCATGGTTGTAAGGAAACAATTACG 59.429 40.000 0.00 0.00 41.18 3.18
4514 5119 7.009540 GCCTGTATACACTGAAATTTGAAATGC 59.990 37.037 0.08 0.00 0.00 3.56
4557 5162 1.209747 GCTGGGGTTATCTCGAGGTTT 59.790 52.381 13.56 0.50 0.00 3.27
4596 5202 6.869315 TTCATTGTTTTGTTGGTAGATCGA 57.131 33.333 0.00 0.00 0.00 3.59
4607 5219 9.825109 TTTGTTGGTAGATCGATGACATAATAA 57.175 29.630 0.54 2.72 0.00 1.40
4693 5312 9.551734 AAAATACTACTACCTCTGTTCGTTTTT 57.448 29.630 0.00 0.00 0.00 1.94
4698 5317 9.852091 ACTACTACCTCTGTTCGTTTTTATAAG 57.148 33.333 0.00 0.00 0.00 1.73
4700 5319 8.754230 ACTACCTCTGTTCGTTTTTATAAGAC 57.246 34.615 0.00 0.00 0.00 3.01
4701 5320 6.701432 ACCTCTGTTCGTTTTTATAAGACG 57.299 37.500 13.97 13.97 38.09 4.18
4702 5321 6.218746 ACCTCTGTTCGTTTTTATAAGACGT 58.781 36.000 17.49 0.00 37.95 4.34
4703 5322 6.703165 ACCTCTGTTCGTTTTTATAAGACGTT 59.297 34.615 17.49 0.00 37.95 3.99
4704 5323 7.225341 ACCTCTGTTCGTTTTTATAAGACGTTT 59.775 33.333 17.49 0.00 37.95 3.60
4705 5324 8.066000 CCTCTGTTCGTTTTTATAAGACGTTTT 58.934 33.333 17.49 0.00 37.95 2.43
4709 5328 9.848172 TGTTCGTTTTTATAAGACGTTTTAGAC 57.152 29.630 17.49 11.04 37.95 2.59
4710 5329 9.848172 GTTCGTTTTTATAAGACGTTTTAGACA 57.152 29.630 17.49 0.00 37.95 3.41
4720 5339 6.920569 AGACGTTTTAGACATTCAAACACT 57.079 33.333 0.00 0.00 31.81 3.55
4721 5340 6.715464 AGACGTTTTAGACATTCAAACACTG 58.285 36.000 0.00 0.00 31.81 3.66
4722 5341 6.315393 AGACGTTTTAGACATTCAAACACTGT 59.685 34.615 0.00 0.00 31.81 3.55
4723 5342 6.848451 ACGTTTTAGACATTCAAACACTGTT 58.152 32.000 0.00 0.00 31.81 3.16
4724 5343 6.964934 ACGTTTTAGACATTCAAACACTGTTC 59.035 34.615 0.00 0.00 31.81 3.18
4725 5344 6.964370 CGTTTTAGACATTCAAACACTGTTCA 59.036 34.615 0.00 0.00 31.81 3.18
4726 5345 7.483375 CGTTTTAGACATTCAAACACTGTTCAA 59.517 33.333 0.00 0.00 31.81 2.69
4727 5346 9.134734 GTTTTAGACATTCAAACACTGTTCAAA 57.865 29.630 0.00 0.00 31.81 2.69
4728 5347 9.698309 TTTTAGACATTCAAACACTGTTCAAAA 57.302 25.926 0.00 0.00 0.00 2.44
4729 5348 8.682128 TTAGACATTCAAACACTGTTCAAAAC 57.318 30.769 0.00 0.00 0.00 2.43
4730 5349 6.686630 AGACATTCAAACACTGTTCAAAACA 58.313 32.000 0.00 0.00 39.52 2.83
4743 5362 4.862018 TGTTCAAAACAGTACAAAGCAAGC 59.138 37.500 0.00 0.00 36.25 4.01
4744 5363 4.981806 TCAAAACAGTACAAAGCAAGCT 57.018 36.364 0.00 0.00 0.00 3.74
4745 5364 4.671377 TCAAAACAGTACAAAGCAAGCTG 58.329 39.130 0.00 0.00 0.00 4.24
4746 5365 4.157656 TCAAAACAGTACAAAGCAAGCTGT 59.842 37.500 0.00 0.00 41.51 4.40
4747 5366 3.971032 AACAGTACAAAGCAAGCTGTC 57.029 42.857 0.00 0.00 39.19 3.51
4748 5367 3.199880 ACAGTACAAAGCAAGCTGTCT 57.800 42.857 0.00 0.00 35.78 3.41
4749 5368 2.874701 ACAGTACAAAGCAAGCTGTCTG 59.125 45.455 0.00 0.00 35.78 3.51
4750 5369 3.133691 CAGTACAAAGCAAGCTGTCTGA 58.866 45.455 0.00 0.00 0.00 3.27
4751 5370 3.561310 CAGTACAAAGCAAGCTGTCTGAA 59.439 43.478 0.00 0.00 0.00 3.02
4752 5371 4.035558 CAGTACAAAGCAAGCTGTCTGAAA 59.964 41.667 0.00 0.00 0.00 2.69
4753 5372 3.427161 ACAAAGCAAGCTGTCTGAAAC 57.573 42.857 0.00 0.00 0.00 2.78
4754 5373 2.223340 ACAAAGCAAGCTGTCTGAAACG 60.223 45.455 0.00 0.00 0.00 3.60
4755 5374 1.668419 AAGCAAGCTGTCTGAAACGT 58.332 45.000 0.00 0.00 0.00 3.99
4756 5375 1.221414 AGCAAGCTGTCTGAAACGTC 58.779 50.000 0.00 0.00 0.00 4.34
4757 5376 1.202580 AGCAAGCTGTCTGAAACGTCT 60.203 47.619 0.00 0.00 0.00 4.18
4758 5377 1.599542 GCAAGCTGTCTGAAACGTCTT 59.400 47.619 0.00 0.00 0.00 3.01
4759 5378 2.800544 GCAAGCTGTCTGAAACGTCTTA 59.199 45.455 0.00 0.00 0.00 2.10
4760 5379 3.433615 GCAAGCTGTCTGAAACGTCTTAT 59.566 43.478 0.00 0.00 0.00 1.73
4761 5380 4.625742 GCAAGCTGTCTGAAACGTCTTATA 59.374 41.667 0.00 0.00 0.00 0.98
4762 5381 5.120208 GCAAGCTGTCTGAAACGTCTTATAA 59.880 40.000 0.00 0.00 0.00 0.98
4763 5382 6.347402 GCAAGCTGTCTGAAACGTCTTATAAA 60.347 38.462 0.00 0.00 0.00 1.40
4764 5383 6.952935 AGCTGTCTGAAACGTCTTATAAAG 57.047 37.500 0.00 0.00 0.00 1.85
4765 5384 6.688578 AGCTGTCTGAAACGTCTTATAAAGA 58.311 36.000 0.00 0.00 34.51 2.52
4778 5397 5.974108 TCTTATAAAGACAAACGGAGGGAG 58.026 41.667 0.00 0.00 31.20 4.30
4786 5405 6.309389 AGACAAACGGAGGGAGTAATAATT 57.691 37.500 0.00 0.00 0.00 1.40
4855 5477 9.539825 AGTGAAATGAACTAGCACTATTATGAG 57.460 33.333 0.00 0.00 37.98 2.90
4856 5478 9.534565 GTGAAATGAACTAGCACTATTATGAGA 57.465 33.333 0.00 0.00 0.00 3.27
4860 5482 6.976088 TGAACTAGCACTATTATGAGAGAGC 58.024 40.000 0.00 0.00 31.92 4.09
4878 5513 3.706086 AGAGCAATTTTGTTCTTGGTGGT 59.294 39.130 4.09 0.00 44.77 4.16
4925 5564 3.128242 CGTAGAGAAGGTAGGAAAGCGAA 59.872 47.826 0.00 0.00 0.00 4.70
4936 5575 1.873591 GGAAAGCGAAGAAGCAAGTGA 59.126 47.619 0.00 0.00 40.15 3.41
4937 5576 2.096019 GGAAAGCGAAGAAGCAAGTGAG 60.096 50.000 0.00 0.00 40.15 3.51
4938 5577 2.533266 AAGCGAAGAAGCAAGTGAGA 57.467 45.000 0.00 0.00 40.15 3.27
4950 5589 3.258123 AGCAAGTGAGAAGAAGAGGAGAC 59.742 47.826 0.00 0.00 0.00 3.36
5040 5681 2.202676 GACTCCTCGAGCCAAGCG 60.203 66.667 6.99 0.00 32.04 4.68
5106 5759 4.394712 CATAGGCGGCGGATCCCC 62.395 72.222 9.78 7.69 0.00 4.81
5155 5810 1.538876 CCACTCCCTCCAGGACCAA 60.539 63.158 0.00 0.00 40.93 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.285401 TGAACTTTTGGTTTGATTTAGAGAGCT 59.715 33.333 0.00 0.00 38.41 4.09
1 2 7.425606 TGAACTTTTGGTTTGATTTAGAGAGC 58.574 34.615 0.00 0.00 38.41 4.09
144 149 6.822442 ACGTGGTATAAATGGTCATATGTGA 58.178 36.000 1.90 0.00 0.00 3.58
406 442 9.581289 TCAATTCTCCTTGTTCTTATACCAAAA 57.419 29.630 0.00 0.00 0.00 2.44
490 536 5.667466 TCATCAAAAGAGTACGGGGTATTC 58.333 41.667 0.00 0.00 0.00 1.75
498 544 7.621832 TGCAAAATTTCATCAAAAGAGTACG 57.378 32.000 0.00 0.00 0.00 3.67
539 585 5.711976 CGGGCATTTGGAGATTTAGGATATT 59.288 40.000 0.00 0.00 0.00 1.28
542 588 3.490348 CGGGCATTTGGAGATTTAGGAT 58.510 45.455 0.00 0.00 0.00 3.24
605 652 4.701651 TGAGACATAGCCTGGTTTTGAATG 59.298 41.667 7.89 0.00 0.00 2.67
644 692 9.764363 ATTCATATTCAACGCTACTAGAATTCA 57.236 29.630 8.44 0.00 33.22 2.57
650 698 5.120830 GGGCATTCATATTCAACGCTACTAG 59.879 44.000 0.00 0.00 0.00 2.57
651 699 4.994852 GGGCATTCATATTCAACGCTACTA 59.005 41.667 0.00 0.00 0.00 1.82
660 708 4.598022 TGAAGTGTGGGCATTCATATTCA 58.402 39.130 0.00 0.00 0.00 2.57
687 797 3.386237 GAGACACGGCCCTGCTCT 61.386 66.667 14.38 10.72 0.00 4.09
785 896 6.322712 ACACCAGATATCTCTTCTCCACTAAC 59.677 42.308 1.03 0.00 0.00 2.34
844 957 2.473070 TGGATGTATTCGGACCTGGAA 58.527 47.619 0.00 0.00 0.00 3.53
866 979 2.398554 CGTTGCGATGGAGGGTTGG 61.399 63.158 0.00 0.00 0.00 3.77
867 980 0.953471 TTCGTTGCGATGGAGGGTTG 60.953 55.000 0.00 0.00 35.23 3.77
868 981 0.250553 TTTCGTTGCGATGGAGGGTT 60.251 50.000 0.00 0.00 35.23 4.11
869 982 0.250553 TTTTCGTTGCGATGGAGGGT 60.251 50.000 0.00 0.00 35.23 4.34
908 1021 2.872818 CAGGGGATGGATGGATGGA 58.127 57.895 0.00 0.00 0.00 3.41
938 1324 4.408821 TGATGGTGCCGTCTGCCC 62.409 66.667 11.28 0.00 40.16 5.36
1239 1629 0.395312 AGACGGTGTTGGTTACCTGG 59.605 55.000 2.07 0.00 36.03 4.45
1259 1650 1.067295 TTGAACTGGAGGCAGTGGAT 58.933 50.000 0.00 0.00 35.30 3.41
1281 1672 1.377536 GCAGAGAGTGGAAATGGAGC 58.622 55.000 0.00 0.00 0.00 4.70
1293 1684 1.859302 ACTCCTAACTGGGCAGAGAG 58.141 55.000 0.00 0.00 36.20 3.20
1295 1686 2.428890 CACTACTCCTAACTGGGCAGAG 59.571 54.545 0.00 0.00 36.20 3.35
1297 1688 1.482593 CCACTACTCCTAACTGGGCAG 59.517 57.143 0.00 0.00 36.20 4.85
1306 1697 2.023695 CCTACCAACCCCACTACTCCTA 60.024 54.545 0.00 0.00 0.00 2.94
1315 1706 1.843851 CTAGCAATCCTACCAACCCCA 59.156 52.381 0.00 0.00 0.00 4.96
1334 1725 3.892588 GGCATCAGTAAGCTCTAGGTACT 59.107 47.826 0.00 0.00 46.37 2.73
1335 1726 3.304794 CGGCATCAGTAAGCTCTAGGTAC 60.305 52.174 0.00 0.00 0.00 3.34
1357 1754 7.851387 AGATCTTTACTAGTTTAGGCTTTGC 57.149 36.000 0.00 0.00 0.00 3.68
1457 1854 8.077991 TGAGACTGATGATGATGTTTTGTTTTC 58.922 33.333 0.00 0.00 0.00 2.29
1474 1874 5.279206 CGGGTGCTTAGATTATGAGACTGAT 60.279 44.000 0.00 0.00 0.00 2.90
1475 1875 4.038042 CGGGTGCTTAGATTATGAGACTGA 59.962 45.833 0.00 0.00 0.00 3.41
1476 1876 4.202161 ACGGGTGCTTAGATTATGAGACTG 60.202 45.833 0.00 0.00 0.00 3.51
1477 1877 3.961408 ACGGGTGCTTAGATTATGAGACT 59.039 43.478 0.00 0.00 0.00 3.24
1478 1878 4.038162 AGACGGGTGCTTAGATTATGAGAC 59.962 45.833 0.00 0.00 0.00 3.36
1484 1884 2.693591 CCTGAGACGGGTGCTTAGATTA 59.306 50.000 0.00 0.00 0.00 1.75
1488 1888 1.115467 ATCCTGAGACGGGTGCTTAG 58.885 55.000 0.00 0.00 0.00 2.18
1512 1912 7.348201 TCAAATTCAACAACAACAACAACAAC 58.652 30.769 0.00 0.00 0.00 3.32
1517 1917 5.005203 GCGATCAAATTCAACAACAACAACA 59.995 36.000 0.00 0.00 0.00 3.33
1518 1918 5.005203 TGCGATCAAATTCAACAACAACAAC 59.995 36.000 0.00 0.00 0.00 3.32
1519 1919 5.105063 TGCGATCAAATTCAACAACAACAA 58.895 33.333 0.00 0.00 0.00 2.83
1520 1920 4.676546 TGCGATCAAATTCAACAACAACA 58.323 34.783 0.00 0.00 0.00 3.33
1521 1921 4.375305 GCTGCGATCAAATTCAACAACAAC 60.375 41.667 0.00 0.00 0.00 3.32
1606 2006 0.035534 TAATCTCAAGCTTGGCGGCA 60.036 50.000 25.73 7.97 34.17 5.69
1636 2036 0.546122 ACCTGTCCTTGACACTGCAA 59.454 50.000 0.00 0.00 37.67 4.08
1690 2090 3.146847 GGGAAGAAAACGACCTCAACAT 58.853 45.455 0.00 0.00 0.00 2.71
1712 2112 2.420129 GCTTAGTTGGTCGGTCCATCAT 60.420 50.000 5.39 0.00 46.60 2.45
1727 2127 1.192146 TCGGTTGGGAGCTGCTTAGT 61.192 55.000 2.53 0.00 0.00 2.24
1810 2210 2.026449 CAGAAGATGCCTCACCTTTCCT 60.026 50.000 0.00 0.00 0.00 3.36
1874 2274 7.341769 CCTTGTTGATAATTGTTAGGAATGGGA 59.658 37.037 0.00 0.00 0.00 4.37
1878 2278 8.893563 TTCCCTTGTTGATAATTGTTAGGAAT 57.106 30.769 0.00 0.00 0.00 3.01
1881 2281 6.096846 CCCTTCCCTTGTTGATAATTGTTAGG 59.903 42.308 0.00 0.00 0.00 2.69
1888 2288 6.136155 CCAATACCCTTCCCTTGTTGATAAT 58.864 40.000 0.00 0.00 0.00 1.28
1901 2301 7.147983 TGCACATATTGTTAACCAATACCCTTC 60.148 37.037 2.48 0.08 46.15 3.46
1930 2490 7.344612 TCTGAGGGCAGAGAACATAAGTTAATA 59.655 37.037 0.00 0.00 45.88 0.98
1931 2491 6.156949 TCTGAGGGCAGAGAACATAAGTTAAT 59.843 38.462 0.00 0.00 45.88 1.40
1950 2510 2.638480 TCCACCAAAACACTCTGAGG 57.362 50.000 9.85 0.76 0.00 3.86
1985 2545 4.724399 TGAAAGCAAGACCAATTCCTGTA 58.276 39.130 0.00 0.00 0.00 2.74
2111 2671 1.037030 TCATCCCTTTTGCGGCATCC 61.037 55.000 2.28 0.00 0.00 3.51
2117 2677 0.532115 CCCCTTTCATCCCTTTTGCG 59.468 55.000 0.00 0.00 0.00 4.85
2162 2722 7.342799 AGCATGTATGAATTGGGTGTCTTATTT 59.657 33.333 0.00 0.00 0.00 1.40
2227 2787 7.771826 AGAGTAGAGACACATAGTTACTTCTCC 59.228 40.741 7.23 0.00 34.30 3.71
2236 2796 7.492020 CACTTACGTAGAGTAGAGACACATAGT 59.508 40.741 9.19 0.00 36.56 2.12
2238 2798 7.277319 CACACTTACGTAGAGTAGAGACACATA 59.723 40.741 9.19 0.00 36.56 2.29
2255 2815 4.103357 AGAAGTAATAGCGCACACTTACG 58.897 43.478 11.47 0.00 31.57 3.18
2396 2956 2.238646 AGATATTGTTCCGCCTGTTCCA 59.761 45.455 0.00 0.00 0.00 3.53
2402 2962 1.747206 GCACCAGATATTGTTCCGCCT 60.747 52.381 0.00 0.00 0.00 5.52
2539 3101 7.368059 GGTTCAACACCAATAACCTAGAAAAG 58.632 38.462 0.00 0.00 46.42 2.27
2617 3179 6.641169 AGGAAAACTCAATGGAAGTCTTTC 57.359 37.500 0.00 0.00 0.00 2.62
2694 3258 4.504858 CCTACACAAGCGGATAAGAGTTT 58.495 43.478 0.00 0.00 0.00 2.66
2699 3263 1.583054 GGCCTACACAAGCGGATAAG 58.417 55.000 0.00 0.00 0.00 1.73
2808 3372 7.834881 AAGGTGAAATATACTGACGGATAGA 57.165 36.000 0.00 0.00 0.00 1.98
2932 3496 5.988561 GCATAATAGACCTATCAGCCTATGC 59.011 44.000 11.64 11.64 33.69 3.14
2991 3556 7.000472 ACCACAATAGAACTAGCATATGCAAT 59.000 34.615 28.62 12.35 45.16 3.56
3040 3605 1.293924 GATCCACTCATGCAAGGACG 58.706 55.000 0.00 0.00 32.04 4.79
3072 3637 5.068198 ACATTTGCATTATACCAAGCAGAGG 59.932 40.000 0.00 0.00 38.35 3.69
3085 3650 5.279206 CCACACAACCCTAACATTTGCATTA 60.279 40.000 0.00 0.00 0.00 1.90
3296 3863 2.418692 TCTCAAAAAGAACGCCGCATA 58.581 42.857 0.00 0.00 0.00 3.14
3356 3923 1.918262 TGAGTCATGATTCCCCTGCTT 59.082 47.619 14.93 0.00 0.00 3.91
3357 3924 1.211457 GTGAGTCATGATTCCCCTGCT 59.789 52.381 14.93 0.00 0.00 4.24
3398 3965 4.016444 CACTTAAATAGCAAGCCAAGGGA 58.984 43.478 0.00 0.00 0.00 4.20
3466 4033 2.226330 ACACGCTGCCTATCAAAAACA 58.774 42.857 0.00 0.00 0.00 2.83
3474 4041 1.026718 GGCTCAAACACGCTGCCTAT 61.027 55.000 0.00 0.00 40.36 2.57
3481 4048 2.484264 AGATAAACTGGCTCAAACACGC 59.516 45.455 0.00 0.00 0.00 5.34
3523 4090 6.379417 TGGGATGCATCATACATTTAACAACA 59.621 34.615 27.25 3.81 0.00 3.33
3528 4095 7.286313 TGTACTGGGATGCATCATACATTTAA 58.714 34.615 27.25 7.59 0.00 1.52
3537 4104 5.716228 AGAAAATTTGTACTGGGATGCATCA 59.284 36.000 27.25 8.45 0.00 3.07
3606 4173 4.695928 ACTGAGCCTAAAACCTTTCGATTC 59.304 41.667 0.00 0.00 0.00 2.52
3611 4178 6.231951 AGTTCTACTGAGCCTAAAACCTTTC 58.768 40.000 0.00 0.00 0.00 2.62
3655 4222 2.165030 TGCCTAGTAGTACTGAAACCGC 59.835 50.000 13.29 5.78 0.00 5.68
3657 4224 3.441572 TCGTGCCTAGTAGTACTGAAACC 59.558 47.826 13.29 0.00 0.00 3.27
3673 4240 1.142097 GCTAACTCCTCCTCGTGCC 59.858 63.158 0.00 0.00 0.00 5.01
3691 4258 2.534396 TACCACCTGCCCACCAAGG 61.534 63.158 0.00 0.00 37.03 3.61
3692 4259 1.303317 GTACCACCTGCCCACCAAG 60.303 63.158 0.00 0.00 0.00 3.61
3693 4260 2.836187 GGTACCACCTGCCCACCAA 61.836 63.158 7.15 0.00 34.73 3.67
3763 4346 0.544595 GTGGTCTCCTACACCCTGGT 60.545 60.000 0.00 0.00 32.24 4.00
4029 4624 3.926058 TTTACCACTATCAGCTTCCCC 57.074 47.619 0.00 0.00 0.00 4.81
4071 4666 8.335532 AGTTCTATGAGCTAGAGATATGACAC 57.664 38.462 0.00 0.00 37.75 3.67
4080 4675 6.942532 AGACAAGAGTTCTATGAGCTAGAG 57.057 41.667 0.00 0.00 37.75 2.43
4100 4695 2.096417 CGTCCGTGGATGTTTTCAAGAC 60.096 50.000 0.00 0.00 0.00 3.01
4142 4737 2.254918 TTGTCACGCACACAAAACAG 57.745 45.000 0.00 0.00 33.41 3.16
4156 4751 1.683629 GGGAACACCACCTGTTTGTCA 60.684 52.381 0.00 0.00 43.60 3.58
4252 4847 3.905249 GGAAATGGTCCTCACGCC 58.095 61.111 0.00 0.00 43.98 5.68
4274 4869 2.919807 GCAGAAAAAGCTTCTTCGCCAG 60.920 50.000 14.44 5.82 0.00 4.85
4307 4904 5.064198 CGCCTTATTCTTATTCGGTTTGACA 59.936 40.000 0.00 0.00 0.00 3.58
4311 4909 3.314357 GCCGCCTTATTCTTATTCGGTTT 59.686 43.478 0.00 0.00 37.86 3.27
4394 4992 3.396560 ACCATGCGTATCATCATCACTG 58.603 45.455 0.00 0.00 31.79 3.66
4499 5103 6.908284 CCAAACACAAGCATTTCAAATTTCAG 59.092 34.615 0.00 0.00 0.00 3.02
4557 5162 8.954950 AAACAATGAAATTACAAACACCATCA 57.045 26.923 0.00 0.00 32.46 3.07
4667 5286 9.551734 AAAAACGAACAGAGGTAGTAGTATTTT 57.448 29.630 0.00 0.00 0.00 1.82
4674 5293 9.846248 GTCTTATAAAAACGAACAGAGGTAGTA 57.154 33.333 0.00 0.00 0.00 1.82
4675 5294 7.540055 CGTCTTATAAAAACGAACAGAGGTAGT 59.460 37.037 12.44 0.00 38.65 2.73
4676 5295 7.540055 ACGTCTTATAAAAACGAACAGAGGTAG 59.460 37.037 20.71 0.00 39.59 3.18
4677 5296 7.370383 ACGTCTTATAAAAACGAACAGAGGTA 58.630 34.615 20.71 0.00 39.59 3.08
4678 5297 6.218746 ACGTCTTATAAAAACGAACAGAGGT 58.781 36.000 20.71 6.10 39.59 3.85
4679 5298 6.701432 ACGTCTTATAAAAACGAACAGAGG 57.299 37.500 20.71 5.58 39.59 3.69
4680 5299 8.982925 AAAACGTCTTATAAAAACGAACAGAG 57.017 30.769 20.71 0.00 39.59 3.35
4683 5302 9.848172 GTCTAAAACGTCTTATAAAAACGAACA 57.152 29.630 20.71 7.27 39.59 3.18
4684 5303 9.848172 TGTCTAAAACGTCTTATAAAAACGAAC 57.152 29.630 20.71 11.63 39.59 3.95
4694 5313 9.052759 AGTGTTTGAATGTCTAAAACGTCTTAT 57.947 29.630 0.00 0.00 36.75 1.73
4695 5314 8.332464 CAGTGTTTGAATGTCTAAAACGTCTTA 58.668 33.333 0.00 0.00 36.75 2.10
4696 5315 7.148306 ACAGTGTTTGAATGTCTAAAACGTCTT 60.148 33.333 0.00 0.00 36.75 3.01
4697 5316 6.315393 ACAGTGTTTGAATGTCTAAAACGTCT 59.685 34.615 0.00 0.00 36.75 4.18
4698 5317 6.483687 ACAGTGTTTGAATGTCTAAAACGTC 58.516 36.000 0.00 0.00 36.75 4.34
4699 5318 6.431198 ACAGTGTTTGAATGTCTAAAACGT 57.569 33.333 0.00 0.00 36.75 3.99
4700 5319 6.964370 TGAACAGTGTTTGAATGTCTAAAACG 59.036 34.615 10.45 0.00 36.75 3.60
4701 5320 8.682128 TTGAACAGTGTTTGAATGTCTAAAAC 57.318 30.769 10.45 0.00 34.97 2.43
4702 5321 9.698309 TTTTGAACAGTGTTTGAATGTCTAAAA 57.302 25.926 10.45 3.40 0.00 1.52
4703 5322 9.134734 GTTTTGAACAGTGTTTGAATGTCTAAA 57.865 29.630 10.45 2.56 0.00 1.85
4704 5323 8.300286 TGTTTTGAACAGTGTTTGAATGTCTAA 58.700 29.630 10.45 0.00 36.25 2.10
4705 5324 7.821652 TGTTTTGAACAGTGTTTGAATGTCTA 58.178 30.769 10.45 0.00 36.25 2.59
4706 5325 6.686630 TGTTTTGAACAGTGTTTGAATGTCT 58.313 32.000 10.45 0.00 36.25 3.41
4707 5326 6.942886 TGTTTTGAACAGTGTTTGAATGTC 57.057 33.333 10.45 0.00 36.25 3.06
4720 5339 4.862018 GCTTGCTTTGTACTGTTTTGAACA 59.138 37.500 0.00 0.00 39.52 3.18
4721 5340 5.004726 CAGCTTGCTTTGTACTGTTTTGAAC 59.995 40.000 0.00 0.00 0.00 3.18
4722 5341 5.101628 CAGCTTGCTTTGTACTGTTTTGAA 58.898 37.500 0.00 0.00 0.00 2.69
4723 5342 4.157656 ACAGCTTGCTTTGTACTGTTTTGA 59.842 37.500 0.00 0.00 38.38 2.69
4724 5343 4.423732 ACAGCTTGCTTTGTACTGTTTTG 58.576 39.130 0.00 0.00 38.38 2.44
4725 5344 4.399303 AGACAGCTTGCTTTGTACTGTTTT 59.601 37.500 0.00 0.00 41.45 2.43
4726 5345 3.947834 AGACAGCTTGCTTTGTACTGTTT 59.052 39.130 0.00 0.00 41.45 2.83
4727 5346 3.313526 CAGACAGCTTGCTTTGTACTGTT 59.686 43.478 0.00 0.00 41.45 3.16
4728 5347 2.874701 CAGACAGCTTGCTTTGTACTGT 59.125 45.455 0.00 0.00 43.93 3.55
4729 5348 3.133691 TCAGACAGCTTGCTTTGTACTG 58.866 45.455 0.00 0.00 0.00 2.74
4730 5349 3.475566 TCAGACAGCTTGCTTTGTACT 57.524 42.857 0.00 0.00 0.00 2.73
4731 5350 4.282873 GTTTCAGACAGCTTGCTTTGTAC 58.717 43.478 0.00 0.00 0.00 2.90
4732 5351 3.002246 CGTTTCAGACAGCTTGCTTTGTA 59.998 43.478 0.00 0.00 0.00 2.41
4733 5352 2.223340 CGTTTCAGACAGCTTGCTTTGT 60.223 45.455 0.00 0.00 0.00 2.83
4734 5353 2.223340 ACGTTTCAGACAGCTTGCTTTG 60.223 45.455 0.00 0.00 0.00 2.77
4735 5354 2.017049 ACGTTTCAGACAGCTTGCTTT 58.983 42.857 0.00 0.00 0.00 3.51
4736 5355 1.599542 GACGTTTCAGACAGCTTGCTT 59.400 47.619 0.00 0.00 0.00 3.91
4737 5356 1.202580 AGACGTTTCAGACAGCTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
4738 5357 1.221414 AGACGTTTCAGACAGCTTGC 58.779 50.000 0.00 0.00 0.00 4.01
4739 5358 6.706055 TTATAAGACGTTTCAGACAGCTTG 57.294 37.500 0.00 0.00 0.00 4.01
4740 5359 7.152645 TCTTTATAAGACGTTTCAGACAGCTT 58.847 34.615 0.00 0.00 31.20 3.74
4741 5360 6.688578 TCTTTATAAGACGTTTCAGACAGCT 58.311 36.000 0.00 0.00 31.20 4.24
4742 5361 6.946229 TCTTTATAAGACGTTTCAGACAGC 57.054 37.500 0.00 0.00 31.20 4.40
4755 5374 5.482878 ACTCCCTCCGTTTGTCTTTATAAGA 59.517 40.000 0.00 0.00 34.51 2.10
4756 5375 5.731591 ACTCCCTCCGTTTGTCTTTATAAG 58.268 41.667 0.00 0.00 0.00 1.73
4757 5376 5.750352 ACTCCCTCCGTTTGTCTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
4758 5377 6.855763 TTACTCCCTCCGTTTGTCTTTATA 57.144 37.500 0.00 0.00 0.00 0.98
4759 5378 5.750352 TTACTCCCTCCGTTTGTCTTTAT 57.250 39.130 0.00 0.00 0.00 1.40
4760 5379 5.750352 ATTACTCCCTCCGTTTGTCTTTA 57.250 39.130 0.00 0.00 0.00 1.85
4761 5380 4.635699 ATTACTCCCTCCGTTTGTCTTT 57.364 40.909 0.00 0.00 0.00 2.52
4762 5381 5.750352 TTATTACTCCCTCCGTTTGTCTT 57.250 39.130 0.00 0.00 0.00 3.01
4763 5382 5.952347 ATTATTACTCCCTCCGTTTGTCT 57.048 39.130 0.00 0.00 0.00 3.41
4764 5383 8.672823 ATTAATTATTACTCCCTCCGTTTGTC 57.327 34.615 0.00 0.00 0.00 3.18
4834 5456 8.087750 GCTCTCTCATAATAGTGCTAGTTCATT 58.912 37.037 0.00 0.00 31.28 2.57
4842 5464 7.555554 ACAAAATTGCTCTCTCATAATAGTGCT 59.444 33.333 0.00 0.00 34.24 4.40
4853 5475 5.218139 CACCAAGAACAAAATTGCTCTCTC 58.782 41.667 0.00 0.00 32.82 3.20
4855 5477 4.202151 ACCACCAAGAACAAAATTGCTCTC 60.202 41.667 0.00 0.00 32.82 3.20
4856 5478 3.706086 ACCACCAAGAACAAAATTGCTCT 59.294 39.130 0.00 0.00 35.28 4.09
4860 5482 5.212194 CGAGTACCACCAAGAACAAAATTG 58.788 41.667 0.00 0.00 0.00 2.32
4878 5513 3.125316 CAACGACCCAAGAAAACGAGTA 58.875 45.455 0.00 0.00 0.00 2.59
4925 5564 3.900601 TCCTCTTCTTCTCACTTGCTTCT 59.099 43.478 0.00 0.00 0.00 2.85
4936 5575 2.027929 TCGTCTCGTCTCCTCTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
4937 5576 2.348660 TCGTCTCGTCTCCTCTTCTTC 58.651 52.381 0.00 0.00 0.00 2.87
4938 5577 2.476126 TCGTCTCGTCTCCTCTTCTT 57.524 50.000 0.00 0.00 0.00 2.52
4950 5589 2.200792 ACTGCTCATCATTCGTCTCG 57.799 50.000 0.00 0.00 0.00 4.04
5040 5681 4.700365 GGGCGCCGTGTTTGCTTC 62.700 66.667 22.54 0.00 0.00 3.86
5119 5772 0.903236 GGGTAGGGTTCTCTGTGTCC 59.097 60.000 0.00 0.00 0.00 4.02
5123 5776 1.552719 GGAGTGGGTAGGGTTCTCTGT 60.553 57.143 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.