Multiple sequence alignment - TraesCS3D01G256600

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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 TraesCS3D01G256600 chr3D 100.000 3377 0 0 1 3377 358565976 358562600 0.000000e+00 6237
1 TraesCS3D01G256600 chr3D 78.984 1004 161 34 1020 1990 358504494 358503508 1.020000e-179 640
2 TraesCS3D01G256600 chr3A 89.467 2345 124 45 1 2304 478244232 478241970 0.000000e+00 2848
3 TraesCS3D01G256600 chr3A 83.293 820 51 34 2406 3191 478241764 478240997 0.000000e+00 676
4 TraesCS3D01G256600 chr3A 80.133 750 127 20 1030 1768 477427546 477428284 1.070000e-149 540
5 TraesCS3D01G256600 chr3A 93.333 120 4 2 2296 2414 478241936 478241820 1.250000e-39 174
6 TraesCS3D01G256600 chr3B 93.337 1906 76 17 432 2304 464617665 464615778 0.000000e+00 2769
7 TraesCS3D01G256600 chr3B 93.527 448 21 4 1 446 464619050 464618609 0.000000e+00 660
8 TraesCS3D01G256600 chr3B 86.256 633 37 15 2313 2923 464615742 464615138 2.840000e-180 641
9 TraesCS3D01G256600 chr3B 92.386 197 10 1 2993 3189 464614655 464614464 3.320000e-70 276
10 TraesCS3D01G256600 chr1D 80.127 785 130 18 1005 1773 451063124 451062350 2.280000e-156 562
11 TraesCS3D01G256600 chr1D 76.577 999 181 33 1005 1966 450579207 450580189 1.810000e-137 499
12 TraesCS3D01G256600 chr1D 78.210 771 148 16 1027 1782 450462948 450462183 3.050000e-130 475
13 TraesCS3D01G256600 chr1B 76.977 999 183 35 1005 1966 618316840 618317828 8.300000e-146 527
14 TraesCS3D01G256600 chr1B 78.196 876 145 30 1002 1848 618908054 618907196 4.990000e-143 518
15 TraesCS3D01G256600 chr1B 76.793 1004 176 41 1005 1966 618542995 618543983 8.360000e-141 510
16 TraesCS3D01G256600 chr1B 76.429 997 183 34 1005 1966 618698924 618697945 3.030000e-135 492
17 TraesCS3D01G256600 chr1B 78.340 771 141 21 1027 1782 617968623 617967864 3.050000e-130 475
18 TraesCS3D01G256600 chr1B 77.905 783 145 21 1005 1773 619095570 619094802 2.370000e-126 462
19 TraesCS3D01G256600 chr1A 77.708 794 144 24 996 1773 545851162 545850386 3.970000e-124 455


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 TraesCS3D01G256600 chr3D 358562600 358565976 3376 True 6237.000000 6237 100.000000 1 3377 1 chr3D.!!$R2 3376
1 TraesCS3D01G256600 chr3D 358503508 358504494 986 True 640.000000 640 78.984000 1020 1990 1 chr3D.!!$R1 970
2 TraesCS3D01G256600 chr3A 478240997 478244232 3235 True 1232.666667 2848 88.697667 1 3191 3 chr3A.!!$R1 3190
3 TraesCS3D01G256600 chr3A 477427546 477428284 738 False 540.000000 540 80.133000 1030 1768 1 chr3A.!!$F1 738
4 TraesCS3D01G256600 chr3B 464614464 464619050 4586 True 1086.500000 2769 91.376500 1 3189 4 chr3B.!!$R1 3188
5 TraesCS3D01G256600 chr1D 451062350 451063124 774 True 562.000000 562 80.127000 1005 1773 1 chr1D.!!$R2 768
6 TraesCS3D01G256600 chr1D 450579207 450580189 982 False 499.000000 499 76.577000 1005 1966 1 chr1D.!!$F1 961
7 TraesCS3D01G256600 chr1D 450462183 450462948 765 True 475.000000 475 78.210000 1027 1782 1 chr1D.!!$R1 755
8 TraesCS3D01G256600 chr1B 618316840 618317828 988 False 527.000000 527 76.977000 1005 1966 1 chr1B.!!$F1 961
9 TraesCS3D01G256600 chr1B 618907196 618908054 858 True 518.000000 518 78.196000 1002 1848 1 chr1B.!!$R3 846
10 TraesCS3D01G256600 chr1B 618542995 618543983 988 False 510.000000 510 76.793000 1005 1966 1 chr1B.!!$F2 961
11 TraesCS3D01G256600 chr1B 618697945 618698924 979 True 492.000000 492 76.429000 1005 1966 1 chr1B.!!$R2 961
12 TraesCS3D01G256600 chr1B 617967864 617968623 759 True 475.000000 475 78.340000 1027 1782 1 chr1B.!!$R1 755
13 TraesCS3D01G256600 chr1B 619094802 619095570 768 True 462.000000 462 77.905000 1005 1773 1 chr1B.!!$R4 768
14 TraesCS3D01G256600 chr1A 545850386 545851162 776 True 455.000000 455 77.708000 996 1773 1 chr1A.!!$R1 777

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
887 1875 0.256177 CCTCCTAACCCCCTTGCTTC 59.744 60.0 0.0 0.0 0.0 3.86 F
1956 3019 0.179073 ATTCCGACGAAGGCTGGATG 60.179 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 3223 0.179000 CCACTAAAGGATCAGCGGCT 59.821 55.0 0.00 0.0 0.0 5.52 R
3118 4748 0.033504 AACCAGTGGCAGTACGTGAG 59.966 55.0 9.78 0.0 0.0 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 129 3.056749 AGCCGCGGATTAATTAGAGTAGG 60.057 47.826 33.48 0.00 0.00 3.18
167 177 0.830444 ACCTGACAGACACGCCCTAA 60.830 55.000 3.32 0.00 0.00 2.69
199 209 1.428448 GCTCGTGCTTCACATGTGTA 58.572 50.000 24.63 15.11 36.60 2.90
200 210 1.391485 GCTCGTGCTTCACATGTGTAG 59.609 52.381 23.81 23.81 36.60 2.74
201 211 2.677199 CTCGTGCTTCACATGTGTAGT 58.323 47.619 26.99 0.00 36.60 2.73
202 212 3.833442 CTCGTGCTTCACATGTGTAGTA 58.167 45.455 26.99 22.36 36.60 1.82
203 213 3.571571 TCGTGCTTCACATGTGTAGTAC 58.428 45.455 30.47 30.47 39.11 2.73
204 214 3.254903 TCGTGCTTCACATGTGTAGTACT 59.745 43.478 33.73 0.00 39.85 2.73
205 215 3.364920 CGTGCTTCACATGTGTAGTACTG 59.635 47.826 33.73 26.77 39.85 2.74
305 315 2.092211 CACGAAAATCACGAGCAGTACC 59.908 50.000 0.00 0.00 34.70 3.34
306 316 2.029290 ACGAAAATCACGAGCAGTACCT 60.029 45.455 0.00 0.00 34.70 3.08
419 431 6.292389 ACGCAGAGAGCATATTGTATTTTC 57.708 37.500 0.00 0.00 46.13 2.29
496 1468 2.791383 CGAGGAGATTGATTCGCTCT 57.209 50.000 0.00 0.00 0.00 4.09
497 1469 2.660490 CGAGGAGATTGATTCGCTCTC 58.340 52.381 6.71 6.71 35.69 3.20
506 1478 0.391661 GATTCGCTCTCAGTGGGCAA 60.392 55.000 0.00 0.00 0.00 4.52
528 1502 6.311200 GCAAAAATAACAATGACAGTGGGATC 59.689 38.462 7.92 0.00 0.00 3.36
533 1507 1.679680 CAATGACAGTGGGATCCATGC 59.320 52.381 15.23 2.56 35.28 4.06
581 1565 1.752358 GCGGAGAGGAGATGGATGCA 61.752 60.000 0.00 0.00 0.00 3.96
681 1665 1.032657 CGTTCCCACCCACACAAACA 61.033 55.000 0.00 0.00 0.00 2.83
683 1667 1.032657 TTCCCACCCACACAAACACG 61.033 55.000 0.00 0.00 0.00 4.49
769 1753 1.733402 TTTGTGCCTCGCCAAGTTGG 61.733 55.000 18.17 18.17 41.55 3.77
880 1868 1.696674 CCTTCCCCTCCTAACCCCC 60.697 68.421 0.00 0.00 0.00 5.40
885 1873 1.619669 CCCTCCTAACCCCCTTGCT 60.620 63.158 0.00 0.00 0.00 3.91
886 1874 1.214992 CCCTCCTAACCCCCTTGCTT 61.215 60.000 0.00 0.00 0.00 3.91
887 1875 0.256177 CCTCCTAACCCCCTTGCTTC 59.744 60.000 0.00 0.00 0.00 3.86
888 1876 0.256177 CTCCTAACCCCCTTGCTTCC 59.744 60.000 0.00 0.00 0.00 3.46
889 1877 0.476808 TCCTAACCCCCTTGCTTCCA 60.477 55.000 0.00 0.00 0.00 3.53
941 1929 2.206536 CCACCCAAACCCAACGCAT 61.207 57.895 0.00 0.00 0.00 4.73
954 1942 3.492756 CCCAACGCATACCAAACAAAAAG 59.507 43.478 0.00 0.00 0.00 2.27
963 1951 7.179410 GCATACCAAACAAAAAGAACAACAAG 58.821 34.615 0.00 0.00 0.00 3.16
976 1964 1.072331 ACAACAAGAAGATCACCGGCT 59.928 47.619 0.00 0.00 0.00 5.52
979 1967 1.338200 ACAAGAAGATCACCGGCTCAC 60.338 52.381 0.00 0.00 0.00 3.51
981 1969 0.904865 AGAAGATCACCGGCTCACCA 60.905 55.000 0.00 0.00 34.57 4.17
986 1991 4.248842 CACCGGCTCACCACCACA 62.249 66.667 0.00 0.00 34.57 4.17
1626 2659 1.153429 GGATAACGTCCTTGCCGCT 60.153 57.895 0.00 0.00 44.16 5.52
1824 2872 1.004440 GTCTCCCAAGAGCACGCTT 60.004 57.895 0.00 0.00 40.22 4.68
1865 2913 1.341187 GGAGACCGAAGAGGAAGAGGA 60.341 57.143 0.00 0.00 45.00 3.71
1866 2914 2.021457 GAGACCGAAGAGGAAGAGGAG 58.979 57.143 0.00 0.00 45.00 3.69
1867 2915 1.107945 GACCGAAGAGGAAGAGGAGG 58.892 60.000 0.00 0.00 45.00 4.30
1868 2916 0.705253 ACCGAAGAGGAAGAGGAGGA 59.295 55.000 0.00 0.00 45.00 3.71
1869 2917 1.341581 ACCGAAGAGGAAGAGGAGGAG 60.342 57.143 0.00 0.00 45.00 3.69
1870 2918 1.398692 CGAAGAGGAAGAGGAGGAGG 58.601 60.000 0.00 0.00 0.00 4.30
1956 3019 0.179073 ATTCCGACGAAGGCTGGATG 60.179 55.000 0.00 0.00 0.00 3.51
2097 3166 3.110178 GTCGTCGGCACCCTTTCG 61.110 66.667 0.00 0.00 0.00 3.46
2130 3199 2.027285 TGAATTGGACGCAGAGGATGAA 60.027 45.455 0.00 0.00 0.00 2.57
2169 3238 2.082140 TCCTAGCCGCTGATCCTTTA 57.918 50.000 2.16 0.00 0.00 1.85
2191 3260 2.125512 ACCGCCAGATCGAAGTGC 60.126 61.111 0.00 0.00 0.00 4.40
2194 3263 2.508891 CGCCAGATCGAAGTGCGTC 61.509 63.158 12.06 0.00 40.33 5.19
2202 3271 2.876645 GAAGTGCGTCCGAGCTCG 60.877 66.667 29.06 29.06 38.13 5.03
2374 3486 4.168101 TCCCTCTTTACACTCCAACTCAT 58.832 43.478 0.00 0.00 0.00 2.90
2421 3599 5.766670 ACACAACTACAGTACTACAGTAGCA 59.233 40.000 15.32 0.00 40.52 3.49
2429 3607 9.761504 CTACAGTACTACAGTAGCAGATAAGTA 57.238 37.037 7.57 2.10 32.73 2.24
2438 3616 3.328382 AGCAGATAAGTAACCACGCAA 57.672 42.857 0.00 0.00 0.00 4.85
2455 3638 2.871022 CGCAATAGAGAAGAGCATTGCT 59.129 45.455 11.79 11.79 47.00 3.91
2464 3647 0.606604 AGAGCATTGCTTTTGCCTGG 59.393 50.000 13.35 0.00 46.87 4.45
2477 3660 2.109799 CCTGGGATAGCACGGCAG 59.890 66.667 0.00 0.00 0.00 4.85
2510 3696 4.099419 ACCCACAAAATGACTGTTTCCTTC 59.901 41.667 0.00 0.00 0.00 3.46
2511 3697 4.501400 CCCACAAAATGACTGTTTCCTTCC 60.501 45.833 0.00 0.00 0.00 3.46
2589 3775 3.354948 TTCCATCTTCCATCACAGGTG 57.645 47.619 0.00 0.00 0.00 4.00
2673 3867 4.457496 CAGCCCACGCCATCTCGT 62.457 66.667 0.00 0.00 44.35 4.18
2734 3942 1.927569 GAAGAAAGCCTCCCCTCCCC 61.928 65.000 0.00 0.00 0.00 4.81
2791 3999 2.042831 CGCTCAAGCAAAGGGGGAG 61.043 63.158 2.50 0.00 42.21 4.30
2792 4000 1.380302 GCTCAAGCAAAGGGGGAGA 59.620 57.895 0.00 0.00 41.59 3.71
2793 4001 0.251341 GCTCAAGCAAAGGGGGAGAA 60.251 55.000 0.00 0.00 41.59 2.87
2794 4002 1.823250 GCTCAAGCAAAGGGGGAGAAA 60.823 52.381 0.00 0.00 41.59 2.52
2795 4003 2.597455 CTCAAGCAAAGGGGGAGAAAA 58.403 47.619 0.00 0.00 0.00 2.29
2796 4004 2.560105 CTCAAGCAAAGGGGGAGAAAAG 59.440 50.000 0.00 0.00 0.00 2.27
2797 4005 2.176798 TCAAGCAAAGGGGGAGAAAAGA 59.823 45.455 0.00 0.00 0.00 2.52
2798 4006 2.965147 CAAGCAAAGGGGGAGAAAAGAA 59.035 45.455 0.00 0.00 0.00 2.52
2799 4007 3.328535 AGCAAAGGGGGAGAAAAGAAA 57.671 42.857 0.00 0.00 0.00 2.52
2800 4008 3.653164 AGCAAAGGGGGAGAAAAGAAAA 58.347 40.909 0.00 0.00 0.00 2.29
2803 4011 4.100963 GCAAAGGGGGAGAAAAGAAAAGAA 59.899 41.667 0.00 0.00 0.00 2.52
2829 4038 3.001406 AAGGAAGCCGTACCCGCT 61.001 61.111 0.00 0.00 0.00 5.52
2877 4090 4.952335 GGGAAAATGGGATATATGCCTCTG 59.048 45.833 22.33 0.00 39.30 3.35
2978 4585 3.005539 GCACCTCTGGCCTCTGGA 61.006 66.667 3.32 0.00 0.00 3.86
2988 4618 4.181010 CCTCTGGACATGGGGCCG 62.181 72.222 0.00 0.00 0.00 6.13
3046 4676 3.529341 TTCCATCACGCCGCACTGT 62.529 57.895 0.00 0.00 0.00 3.55
3060 4690 1.062587 GCACTGTTACCACATGCGATC 59.937 52.381 0.00 0.00 31.88 3.69
3073 4703 1.062047 GCGATCAGTACGAGCACGA 59.938 57.895 11.40 0.00 42.66 4.35
3116 4746 2.047655 GTGATTGTCCGGCCGTCA 60.048 61.111 26.12 17.98 0.00 4.35
3117 4747 2.047655 TGATTGTCCGGCCGTCAC 60.048 61.111 26.12 20.30 0.00 3.67
3118 4748 2.818274 GATTGTCCGGCCGTCACC 60.818 66.667 26.12 12.72 0.00 4.02
3119 4749 3.310860 GATTGTCCGGCCGTCACCT 62.311 63.158 26.12 12.20 0.00 4.00
3120 4750 3.310860 ATTGTCCGGCCGTCACCTC 62.311 63.158 26.12 7.87 0.00 3.85
3127 4757 2.633509 GGCCGTCACCTCACGTACT 61.634 63.158 0.00 0.00 38.14 2.73
3201 4831 3.170362 CCCTGAGGCCAACTCCAA 58.830 61.111 5.01 0.00 46.01 3.53
3202 4832 1.693640 CCCTGAGGCCAACTCCAAT 59.306 57.895 5.01 0.00 46.01 3.16
3203 4833 0.682209 CCCTGAGGCCAACTCCAATG 60.682 60.000 5.01 0.00 46.01 2.82
3204 4834 0.038744 CCTGAGGCCAACTCCAATGT 59.961 55.000 5.01 0.00 46.01 2.71
3205 4835 1.171308 CTGAGGCCAACTCCAATGTG 58.829 55.000 5.01 0.00 46.01 3.21
3206 4836 0.895100 TGAGGCCAACTCCAATGTGC 60.895 55.000 5.01 0.00 46.01 4.57
3207 4837 1.926511 GAGGCCAACTCCAATGTGCG 61.927 60.000 5.01 0.00 40.49 5.34
3208 4838 1.971167 GGCCAACTCCAATGTGCGA 60.971 57.895 0.00 0.00 0.00 5.10
3209 4839 1.210155 GCCAACTCCAATGTGCGAC 59.790 57.895 0.00 0.00 0.00 5.19
3210 4840 1.237285 GCCAACTCCAATGTGCGACT 61.237 55.000 0.00 0.00 0.00 4.18
3211 4841 0.798776 CCAACTCCAATGTGCGACTC 59.201 55.000 0.00 0.00 0.00 3.36
3212 4842 0.798776 CAACTCCAATGTGCGACTCC 59.201 55.000 0.00 0.00 0.00 3.85
3213 4843 0.396435 AACTCCAATGTGCGACTCCA 59.604 50.000 0.00 0.00 0.00 3.86
3214 4844 0.615331 ACTCCAATGTGCGACTCCAT 59.385 50.000 0.00 0.00 0.00 3.41
3215 4845 1.293924 CTCCAATGTGCGACTCCATC 58.706 55.000 0.00 0.00 0.00 3.51
3216 4846 0.612744 TCCAATGTGCGACTCCATCA 59.387 50.000 0.00 0.00 0.00 3.07
3217 4847 1.210234 TCCAATGTGCGACTCCATCAT 59.790 47.619 0.00 0.00 0.00 2.45
3218 4848 1.332686 CCAATGTGCGACTCCATCATG 59.667 52.381 0.00 0.00 0.00 3.07
3219 4849 2.011947 CAATGTGCGACTCCATCATGT 58.988 47.619 0.00 0.00 0.00 3.21
3220 4850 1.945387 ATGTGCGACTCCATCATGTC 58.055 50.000 0.00 0.00 0.00 3.06
3221 4851 0.108186 TGTGCGACTCCATCATGTCC 60.108 55.000 0.00 0.00 0.00 4.02
3222 4852 1.141665 TGCGACTCCATCATGTCCG 59.858 57.895 0.00 0.00 0.00 4.79
3223 4853 2.240500 GCGACTCCATCATGTCCGC 61.241 63.158 0.00 0.00 0.00 5.54
3224 4854 1.439228 CGACTCCATCATGTCCGCT 59.561 57.895 0.00 0.00 0.00 5.52
3225 4855 0.179100 CGACTCCATCATGTCCGCTT 60.179 55.000 0.00 0.00 0.00 4.68
3226 4856 1.576356 GACTCCATCATGTCCGCTTC 58.424 55.000 0.00 0.00 0.00 3.86
3227 4857 0.179100 ACTCCATCATGTCCGCTTCG 60.179 55.000 0.00 0.00 0.00 3.79
3228 4858 0.179100 CTCCATCATGTCCGCTTCGT 60.179 55.000 0.00 0.00 0.00 3.85
3229 4859 0.249120 TCCATCATGTCCGCTTCGTT 59.751 50.000 0.00 0.00 0.00 3.85
3230 4860 1.086696 CCATCATGTCCGCTTCGTTT 58.913 50.000 0.00 0.00 0.00 3.60
3231 4861 1.202065 CCATCATGTCCGCTTCGTTTG 60.202 52.381 0.00 0.00 0.00 2.93
3232 4862 0.447801 ATCATGTCCGCTTCGTTTGC 59.552 50.000 0.00 0.00 0.00 3.68
3233 4863 0.882484 TCATGTCCGCTTCGTTTGCA 60.882 50.000 0.00 0.00 0.00 4.08
3234 4864 0.168788 CATGTCCGCTTCGTTTGCAT 59.831 50.000 0.00 0.00 0.00 3.96
3235 4865 0.447801 ATGTCCGCTTCGTTTGCATC 59.552 50.000 0.00 0.00 0.00 3.91
3236 4866 0.882484 TGTCCGCTTCGTTTGCATCA 60.882 50.000 0.00 0.00 0.00 3.07
3237 4867 0.237235 GTCCGCTTCGTTTGCATCAA 59.763 50.000 0.00 0.00 0.00 2.57
3238 4868 0.947960 TCCGCTTCGTTTGCATCAAA 59.052 45.000 0.00 0.00 0.00 2.69
3239 4869 1.335182 TCCGCTTCGTTTGCATCAAAA 59.665 42.857 0.00 0.00 35.03 2.44
3240 4870 1.451651 CCGCTTCGTTTGCATCAAAAC 59.548 47.619 0.00 0.00 35.03 2.43
3255 4885 8.144155 TGCATCAAAACGGATAAATAATACGA 57.856 30.769 0.00 0.00 45.47 3.43
3256 4886 8.065407 TGCATCAAAACGGATAAATAATACGAC 58.935 33.333 0.00 0.00 45.47 4.34
3257 4887 8.280497 GCATCAAAACGGATAAATAATACGACT 58.720 33.333 0.00 0.00 45.47 4.18
3258 4888 9.793245 CATCAAAACGGATAAATAATACGACTC 57.207 33.333 0.00 0.00 45.47 3.36
3259 4889 8.929827 TCAAAACGGATAAATAATACGACTCA 57.070 30.769 0.00 0.00 45.47 3.41
3260 4890 9.368674 TCAAAACGGATAAATAATACGACTCAA 57.631 29.630 0.00 0.00 45.47 3.02
3261 4891 9.417284 CAAAACGGATAAATAATACGACTCAAC 57.583 33.333 0.00 0.00 45.47 3.18
3262 4892 6.981379 ACGGATAAATAATACGACTCAACG 57.019 37.500 0.00 0.00 45.47 4.10
3263 4893 5.400485 ACGGATAAATAATACGACTCAACGC 59.600 40.000 0.00 0.00 45.47 4.84
3264 4894 5.441099 CGGATAAATAATACGACTCAACGCG 60.441 44.000 3.53 3.53 45.47 6.01
3265 4895 3.564408 AAATAATACGACTCAACGCGC 57.436 42.857 5.73 0.00 36.70 6.86
3266 4896 2.197792 ATAATACGACTCAACGCGCA 57.802 45.000 5.73 0.00 36.70 6.09
3267 4897 1.979897 TAATACGACTCAACGCGCAA 58.020 45.000 5.73 0.00 36.70 4.85
3268 4898 0.437295 AATACGACTCAACGCGCAAC 59.563 50.000 5.73 0.00 36.70 4.17
3269 4899 1.349259 ATACGACTCAACGCGCAACC 61.349 55.000 5.73 0.00 36.70 3.77
3270 4900 4.409588 CGACTCAACGCGCAACCG 62.410 66.667 5.73 0.00 37.57 4.44
3284 4914 4.901866 CGCAACCGCATTCTTAAATTTT 57.098 36.364 0.00 0.00 38.40 1.82
3285 4915 4.627098 CGCAACCGCATTCTTAAATTTTG 58.373 39.130 0.00 0.00 38.40 2.44
3286 4916 4.149747 CGCAACCGCATTCTTAAATTTTGT 59.850 37.500 0.00 0.00 38.40 2.83
3287 4917 5.608146 GCAACCGCATTCTTAAATTTTGTC 58.392 37.500 0.00 0.00 38.36 3.18
3288 4918 5.389411 GCAACCGCATTCTTAAATTTTGTCC 60.389 40.000 0.00 0.00 38.36 4.02
3289 4919 4.816392 ACCGCATTCTTAAATTTTGTCCC 58.184 39.130 0.00 0.00 0.00 4.46
3290 4920 4.526650 ACCGCATTCTTAAATTTTGTCCCT 59.473 37.500 0.00 0.00 0.00 4.20
3291 4921 5.011635 ACCGCATTCTTAAATTTTGTCCCTT 59.988 36.000 0.00 0.00 0.00 3.95
3292 4922 5.576774 CCGCATTCTTAAATTTTGTCCCTTC 59.423 40.000 0.00 0.00 0.00 3.46
3293 4923 5.286082 CGCATTCTTAAATTTTGTCCCTTCG 59.714 40.000 0.00 0.00 0.00 3.79
3294 4924 5.576774 GCATTCTTAAATTTTGTCCCTTCGG 59.423 40.000 0.00 0.00 0.00 4.30
3295 4925 4.776795 TCTTAAATTTTGTCCCTTCGGC 57.223 40.909 0.00 0.00 0.00 5.54
3296 4926 4.145807 TCTTAAATTTTGTCCCTTCGGCA 58.854 39.130 0.00 0.00 0.00 5.69
3297 4927 4.770010 TCTTAAATTTTGTCCCTTCGGCAT 59.230 37.500 0.00 0.00 0.00 4.40
3298 4928 3.592898 AAATTTTGTCCCTTCGGCATC 57.407 42.857 0.00 0.00 0.00 3.91
3299 4929 1.474330 ATTTTGTCCCTTCGGCATCC 58.526 50.000 0.00 0.00 0.00 3.51
3312 4942 2.516930 CATCCGGCTCGCCCAATT 60.517 61.111 0.00 0.00 0.00 2.32
3313 4943 2.120909 CATCCGGCTCGCCCAATTT 61.121 57.895 0.00 0.00 0.00 1.82
3314 4944 1.823899 ATCCGGCTCGCCCAATTTC 60.824 57.895 0.00 0.00 0.00 2.17
3315 4945 3.518068 CCGGCTCGCCCAATTTCC 61.518 66.667 1.72 0.00 0.00 3.13
3316 4946 3.876198 CGGCTCGCCCAATTTCCG 61.876 66.667 1.72 0.00 0.00 4.30
3317 4947 3.518068 GGCTCGCCCAATTTCCGG 61.518 66.667 0.00 0.00 0.00 5.14
3318 4948 4.193334 GCTCGCCCAATTTCCGGC 62.193 66.667 0.00 0.00 42.05 6.13
3322 4952 4.062656 GCCCAATTTCCGGCGCAA 62.063 61.111 10.83 0.00 34.94 4.85
3323 4953 2.653702 CCCAATTTCCGGCGCAAA 59.346 55.556 10.83 0.00 0.00 3.68
3324 4954 1.736282 CCCAATTTCCGGCGCAAAC 60.736 57.895 10.83 0.00 0.00 2.93
3325 4955 1.006805 CCAATTTCCGGCGCAAACA 60.007 52.632 10.83 0.00 0.00 2.83
3326 4956 0.389687 CCAATTTCCGGCGCAAACAT 60.390 50.000 10.83 0.00 0.00 2.71
3327 4957 0.714994 CAATTTCCGGCGCAAACATG 59.285 50.000 10.83 0.00 0.00 3.21
3328 4958 1.013524 AATTTCCGGCGCAAACATGC 61.014 50.000 10.83 0.00 0.00 4.06
3336 4966 4.895854 GCAAACATGCGCCAGATT 57.104 50.000 4.18 0.00 0.00 2.40
3337 4967 3.126729 GCAAACATGCGCCAGATTT 57.873 47.368 4.18 0.00 0.00 2.17
3338 4968 0.717224 GCAAACATGCGCCAGATTTG 59.283 50.000 4.18 11.69 34.17 2.32
3339 4969 0.717224 CAAACATGCGCCAGATTTGC 59.283 50.000 4.18 0.00 0.00 3.68
3346 4976 3.667087 GCCAGATTTGCGACCACA 58.333 55.556 0.00 0.00 0.00 4.17
3347 4977 2.183409 GCCAGATTTGCGACCACAT 58.817 52.632 0.00 0.00 0.00 3.21
3348 4978 0.179156 GCCAGATTTGCGACCACATG 60.179 55.000 0.00 0.00 0.00 3.21
3349 4979 0.452987 CCAGATTTGCGACCACATGG 59.547 55.000 0.00 0.00 42.17 3.66
3350 4980 1.452110 CAGATTTGCGACCACATGGA 58.548 50.000 4.53 0.00 38.94 3.41
3351 4981 1.131126 CAGATTTGCGACCACATGGAC 59.869 52.381 4.53 0.00 38.94 4.02
3356 4986 2.257371 CGACCACATGGACGTCGT 59.743 61.111 18.02 0.00 45.60 4.34
3357 4987 1.800315 CGACCACATGGACGTCGTC 60.800 63.158 17.16 17.16 45.60 4.20
3358 4988 1.800315 GACCACATGGACGTCGTCG 60.800 63.158 18.61 8.12 39.85 5.12
3359 4989 2.191354 GACCACATGGACGTCGTCGA 62.191 60.000 18.61 15.72 38.40 4.20
3360 4990 1.081041 CCACATGGACGTCGTCGAA 60.081 57.895 18.61 10.26 40.62 3.71
3361 4991 1.342082 CCACATGGACGTCGTCGAAC 61.342 60.000 18.61 6.26 40.62 3.95
3363 4993 2.150218 CATGGACGTCGTCGAACGG 61.150 63.158 18.61 6.07 46.72 4.44
3364 4994 2.327343 ATGGACGTCGTCGAACGGA 61.327 57.895 18.61 0.00 46.72 4.69
3365 4995 2.500582 GGACGTCGTCGAACGGAC 60.501 66.667 18.61 8.24 46.72 4.79
3372 5002 3.749373 GTCGAACGGACGTGCACG 61.749 66.667 35.99 35.99 46.33 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.741055 CGCCCACTTAAATCAGCGGTA 60.741 52.381 0.00 0.00 39.89 4.02
72 78 0.108041 TGAGGTCGTTAATTCCGGGC 60.108 55.000 0.00 0.00 0.00 6.13
167 177 1.014044 CACGAGCGTGGTTAGTGCAT 61.014 55.000 14.73 0.00 42.00 3.96
200 210 6.458342 GCCAAAATAGATGCAAGTACCAGTAC 60.458 42.308 0.00 0.00 36.35 2.73
201 211 5.588648 GCCAAAATAGATGCAAGTACCAGTA 59.411 40.000 0.00 0.00 0.00 2.74
202 212 4.399303 GCCAAAATAGATGCAAGTACCAGT 59.601 41.667 0.00 0.00 0.00 4.00
203 213 4.641989 AGCCAAAATAGATGCAAGTACCAG 59.358 41.667 0.00 0.00 0.00 4.00
204 214 4.599041 AGCCAAAATAGATGCAAGTACCA 58.401 39.130 0.00 0.00 0.00 3.25
205 215 4.640201 TGAGCCAAAATAGATGCAAGTACC 59.360 41.667 0.00 0.00 0.00 3.34
246 256 1.623359 GAGCGTCAGTACAGAGCAAG 58.377 55.000 10.61 0.00 0.00 4.01
404 416 5.300286 GTGAGGCCAGAAAATACAATATGCT 59.700 40.000 5.01 0.00 0.00 3.79
419 431 0.397941 TCTCCTTTGTGTGAGGCCAG 59.602 55.000 5.01 0.00 34.17 4.85
495 1467 5.634859 GTCATTGTTATTTTTGCCCACTGAG 59.365 40.000 0.00 0.00 0.00 3.35
496 1468 5.069648 TGTCATTGTTATTTTTGCCCACTGA 59.930 36.000 0.00 0.00 0.00 3.41
497 1469 5.295950 TGTCATTGTTATTTTTGCCCACTG 58.704 37.500 0.00 0.00 0.00 3.66
506 1478 6.015918 TGGATCCCACTGTCATTGTTATTTT 58.984 36.000 9.90 0.00 0.00 1.82
528 1502 4.124351 CAGGCACTTGGCGCATGG 62.124 66.667 10.83 0.00 46.16 3.66
581 1565 2.876955 CACATGCCGCCGTCAAAT 59.123 55.556 0.00 0.00 0.00 2.32
697 1681 4.119136 CAATTGGACGCTGTTTCCTTTTT 58.881 39.130 0.00 0.00 33.84 1.94
698 1682 3.716601 CAATTGGACGCTGTTTCCTTTT 58.283 40.909 0.00 0.00 33.84 2.27
753 1737 3.365265 CCCAACTTGGCGAGGCAC 61.365 66.667 6.71 0.00 35.79 5.01
769 1753 1.135915 TGTTTGGTGTGTGTCAATGCC 59.864 47.619 0.00 0.00 0.00 4.40
888 1876 5.501715 GCGCGTTTATATATCCATGGAATG 58.498 41.667 20.67 6.87 46.21 2.67
889 1877 4.270084 CGCGCGTTTATATATCCATGGAAT 59.730 41.667 24.19 15.39 0.00 3.01
941 1929 8.361139 TCTTCTTGTTGTTCTTTTTGTTTGGTA 58.639 29.630 0.00 0.00 0.00 3.25
954 1942 2.095718 GCCGGTGATCTTCTTGTTGTTC 60.096 50.000 1.90 0.00 0.00 3.18
963 1951 0.741221 GTGGTGAGCCGGTGATCTTC 60.741 60.000 1.90 0.00 37.67 2.87
976 1964 0.463654 GCTTGTCTGTGTGGTGGTGA 60.464 55.000 0.00 0.00 0.00 4.02
979 1967 0.664761 CTTGCTTGTCTGTGTGGTGG 59.335 55.000 0.00 0.00 0.00 4.61
981 1969 2.418368 TTCTTGCTTGTCTGTGTGGT 57.582 45.000 0.00 0.00 0.00 4.16
986 1991 0.877071 CGCCATTCTTGCTTGTCTGT 59.123 50.000 0.00 0.00 0.00 3.41
1596 2626 1.494721 ACGTTATCCATCTTGCCCCAT 59.505 47.619 0.00 0.00 0.00 4.00
1611 2641 1.373748 GACAGCGGCAAGGACGTTA 60.374 57.895 1.45 0.00 35.91 3.18
1626 2659 2.053865 GTACCCGATCCGGTGGACA 61.054 63.158 15.15 0.00 46.80 4.02
1677 2710 2.103934 CTCTTCGCCTCCGCTGAG 59.896 66.667 0.00 0.00 38.42 3.35
1824 2872 2.535485 ATTCCCAGAATGCGGCGTCA 62.535 55.000 9.37 7.70 31.97 4.35
1865 2913 1.719378 TCTCTGAAACCTCCTCCTCCT 59.281 52.381 0.00 0.00 0.00 3.69
1866 2914 2.107366 CTCTCTGAAACCTCCTCCTCC 58.893 57.143 0.00 0.00 0.00 4.30
1867 2915 1.480545 GCTCTCTGAAACCTCCTCCTC 59.519 57.143 0.00 0.00 0.00 3.71
1868 2916 1.567357 GCTCTCTGAAACCTCCTCCT 58.433 55.000 0.00 0.00 0.00 3.69
1869 2917 0.539518 GGCTCTCTGAAACCTCCTCC 59.460 60.000 0.00 0.00 0.00 4.30
1870 2918 0.539518 GGGCTCTCTGAAACCTCCTC 59.460 60.000 0.00 0.00 0.00 3.71
2097 3166 4.728882 GCGTCCAATTCATGTTCATCACTC 60.729 45.833 0.00 0.00 0.00 3.51
2139 3208 1.532090 GCGGCTAGGATGATATCGTCG 60.532 57.143 16.88 7.17 32.78 5.12
2154 3223 0.179000 CCACTAAAGGATCAGCGGCT 59.821 55.000 0.00 0.00 0.00 5.52
2169 3238 1.949847 CTTCGATCTGGCGGTCCACT 61.950 60.000 0.00 0.00 37.47 4.00
2185 3254 2.876645 CGAGCTCGGACGCACTTC 60.877 66.667 28.40 0.00 35.37 3.01
2213 3282 7.344612 AGGGTACATGTGATGATGAAAGTAGTA 59.655 37.037 9.11 0.00 0.00 1.82
2214 3283 6.156949 AGGGTACATGTGATGATGAAAGTAGT 59.843 38.462 9.11 0.00 0.00 2.73
2215 3284 6.481313 CAGGGTACATGTGATGATGAAAGTAG 59.519 42.308 9.11 0.00 0.00 2.57
2421 3599 6.710597 TCTCTATTGCGTGGTTACTTATCT 57.289 37.500 0.00 0.00 0.00 1.98
2429 3607 2.028112 TGCTCTTCTCTATTGCGTGGTT 60.028 45.455 0.00 0.00 0.00 3.67
2438 3616 4.097589 GGCAAAAGCAATGCTCTTCTCTAT 59.902 41.667 8.71 0.00 43.34 1.98
2455 3638 0.679640 CCGTGCTATCCCAGGCAAAA 60.680 55.000 0.00 0.00 40.26 2.44
2464 3647 0.815615 CTTTCCCTGCCGTGCTATCC 60.816 60.000 0.00 0.00 0.00 2.59
2477 3660 4.814234 GTCATTTTGTGGGTTTTCTTTCCC 59.186 41.667 0.00 0.00 43.67 3.97
2493 3676 2.955660 TGCGGAAGGAAACAGTCATTTT 59.044 40.909 0.00 0.00 28.15 1.82
2589 3775 4.867599 GACGATCCGGCCGTGTCC 62.868 72.222 26.12 9.16 40.67 4.02
2673 3867 1.884075 ATCAAGTGGAGGCGTACGCA 61.884 55.000 37.99 18.03 44.11 5.24
2674 3868 0.739813 AATCAAGTGGAGGCGTACGC 60.740 55.000 31.54 31.54 41.06 4.42
2675 3869 2.572191 TAATCAAGTGGAGGCGTACG 57.428 50.000 11.84 11.84 0.00 3.67
2676 3870 4.439057 TCATTAATCAAGTGGAGGCGTAC 58.561 43.478 0.00 0.00 0.00 3.67
2677 3871 4.746535 TCATTAATCAAGTGGAGGCGTA 57.253 40.909 0.00 0.00 0.00 4.42
2678 3872 3.627395 TCATTAATCAAGTGGAGGCGT 57.373 42.857 0.00 0.00 0.00 5.68
2679 3873 4.576053 TCATTCATTAATCAAGTGGAGGCG 59.424 41.667 0.00 0.00 0.00 5.52
2680 3874 6.455360 TTCATTCATTAATCAAGTGGAGGC 57.545 37.500 0.00 0.00 0.00 4.70
2681 3875 7.431249 CCATTCATTCATTAATCAAGTGGAGG 58.569 38.462 0.00 0.00 0.00 4.30
2682 3876 6.921857 GCCATTCATTCATTAATCAAGTGGAG 59.078 38.462 0.00 0.00 0.00 3.86
2793 4001 9.155975 GCTTCCTTCTTTTCTTTTCTTTTCTTT 57.844 29.630 0.00 0.00 0.00 2.52
2794 4002 7.766278 GGCTTCCTTCTTTTCTTTTCTTTTCTT 59.234 33.333 0.00 0.00 0.00 2.52
2795 4003 7.268586 GGCTTCCTTCTTTTCTTTTCTTTTCT 58.731 34.615 0.00 0.00 0.00 2.52
2796 4004 6.199154 CGGCTTCCTTCTTTTCTTTTCTTTTC 59.801 38.462 0.00 0.00 0.00 2.29
2797 4005 6.042777 CGGCTTCCTTCTTTTCTTTTCTTTT 58.957 36.000 0.00 0.00 0.00 2.27
2798 4006 5.127194 ACGGCTTCCTTCTTTTCTTTTCTTT 59.873 36.000 0.00 0.00 0.00 2.52
2799 4007 4.645136 ACGGCTTCCTTCTTTTCTTTTCTT 59.355 37.500 0.00 0.00 0.00 2.52
2800 4008 4.207955 ACGGCTTCCTTCTTTTCTTTTCT 58.792 39.130 0.00 0.00 0.00 2.52
2803 4011 3.819337 GGTACGGCTTCCTTCTTTTCTTT 59.181 43.478 0.00 0.00 0.00 2.52
2829 4038 3.135167 ACCCCTATCGCGAATTAAAAGGA 59.865 43.478 15.24 0.00 0.00 3.36
2924 4137 4.276431 GCTCGCTAGAAGATAGTACAGGTT 59.724 45.833 0.00 0.00 0.00 3.50
2964 4571 1.525923 CATGTCCAGAGGCCAGAGG 59.474 63.158 5.01 2.72 0.00 3.69
3012 4642 0.616891 GGAACCGGTGATACTTGGGT 59.383 55.000 8.52 0.00 0.00 4.51
3017 4647 1.136305 CGTGATGGAACCGGTGATACT 59.864 52.381 8.52 0.00 0.00 2.12
3046 4676 2.424246 TCGTACTGATCGCATGTGGTAA 59.576 45.455 6.39 0.00 0.00 2.85
3060 4690 1.801913 GCCTGTCGTGCTCGTACTG 60.802 63.158 8.17 8.78 38.33 2.74
3097 4727 4.404098 ACGGCCGGACAATCACCC 62.404 66.667 31.76 0.00 0.00 4.61
3116 4746 1.666011 CAGTGGCAGTACGTGAGGT 59.334 57.895 0.00 0.00 0.00 3.85
3117 4747 1.079819 CCAGTGGCAGTACGTGAGG 60.080 63.158 0.00 0.00 0.00 3.86
3118 4748 0.033504 AACCAGTGGCAGTACGTGAG 59.966 55.000 9.78 0.00 0.00 3.51
3119 4749 1.330234 TAACCAGTGGCAGTACGTGA 58.670 50.000 9.78 0.00 0.00 4.35
3120 4750 2.066262 CTTAACCAGTGGCAGTACGTG 58.934 52.381 9.78 0.00 0.00 4.49
3191 4821 1.210155 GTCGCACATTGGAGTTGGC 59.790 57.895 0.00 0.00 0.00 4.52
3192 4822 0.798776 GAGTCGCACATTGGAGTTGG 59.201 55.000 0.00 0.00 0.00 3.77
3193 4823 0.798776 GGAGTCGCACATTGGAGTTG 59.201 55.000 0.00 0.00 0.00 3.16
3194 4824 0.396435 TGGAGTCGCACATTGGAGTT 59.604 50.000 0.00 0.00 0.00 3.01
3195 4825 0.615331 ATGGAGTCGCACATTGGAGT 59.385 50.000 0.00 0.00 0.00 3.85
3196 4826 1.293924 GATGGAGTCGCACATTGGAG 58.706 55.000 0.00 0.00 0.00 3.86
3197 4827 0.612744 TGATGGAGTCGCACATTGGA 59.387 50.000 0.00 0.00 0.00 3.53
3198 4828 1.332686 CATGATGGAGTCGCACATTGG 59.667 52.381 0.00 0.00 0.00 3.16
3199 4829 2.011947 ACATGATGGAGTCGCACATTG 58.988 47.619 0.00 0.00 0.00 2.82
3200 4830 2.283298 GACATGATGGAGTCGCACATT 58.717 47.619 0.00 0.00 0.00 2.71
3201 4831 1.473965 GGACATGATGGAGTCGCACAT 60.474 52.381 0.00 0.00 35.63 3.21
3202 4832 0.108186 GGACATGATGGAGTCGCACA 60.108 55.000 0.00 0.00 35.63 4.57
3203 4833 1.148157 CGGACATGATGGAGTCGCAC 61.148 60.000 0.00 0.00 35.63 5.34
3204 4834 1.141665 CGGACATGATGGAGTCGCA 59.858 57.895 0.00 0.00 35.63 5.10
3205 4835 2.240500 GCGGACATGATGGAGTCGC 61.241 63.158 0.00 3.00 35.63 5.19
3206 4836 0.179100 AAGCGGACATGATGGAGTCG 60.179 55.000 0.00 0.00 35.63 4.18
3207 4837 1.576356 GAAGCGGACATGATGGAGTC 58.424 55.000 0.00 0.00 0.00 3.36
3208 4838 0.179100 CGAAGCGGACATGATGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
3209 4839 0.179100 ACGAAGCGGACATGATGGAG 60.179 55.000 0.00 0.00 0.00 3.86
3210 4840 0.249120 AACGAAGCGGACATGATGGA 59.751 50.000 0.00 0.00 0.00 3.41
3211 4841 1.086696 AAACGAAGCGGACATGATGG 58.913 50.000 0.00 0.00 0.00 3.51
3212 4842 1.791555 GCAAACGAAGCGGACATGATG 60.792 52.381 0.00 0.00 0.00 3.07
3213 4843 0.447801 GCAAACGAAGCGGACATGAT 59.552 50.000 0.00 0.00 0.00 2.45
3214 4844 0.882484 TGCAAACGAAGCGGACATGA 60.882 50.000 0.00 0.00 33.85 3.07
3215 4845 0.168788 ATGCAAACGAAGCGGACATG 59.831 50.000 0.00 0.00 33.85 3.21
3216 4846 0.447801 GATGCAAACGAAGCGGACAT 59.552 50.000 0.00 0.00 33.85 3.06
3217 4847 0.882484 TGATGCAAACGAAGCGGACA 60.882 50.000 0.00 0.00 33.85 4.02
3218 4848 0.237235 TTGATGCAAACGAAGCGGAC 59.763 50.000 0.00 0.00 33.85 4.79
3219 4849 0.947960 TTTGATGCAAACGAAGCGGA 59.052 45.000 0.00 0.00 33.85 5.54
3220 4850 1.451651 GTTTTGATGCAAACGAAGCGG 59.548 47.619 0.00 0.00 32.79 5.52
3221 4851 1.120551 CGTTTTGATGCAAACGAAGCG 59.879 47.619 14.62 14.73 32.79 4.68
3222 4852 1.451651 CCGTTTTGATGCAAACGAAGC 59.548 47.619 19.98 10.73 32.79 3.86
3223 4853 2.993545 TCCGTTTTGATGCAAACGAAG 58.006 42.857 19.98 7.04 32.79 3.79
3224 4854 3.634568 ATCCGTTTTGATGCAAACGAA 57.365 38.095 19.98 2.92 32.79 3.85
3225 4855 4.750952 TTATCCGTTTTGATGCAAACGA 57.249 36.364 19.98 8.80 32.79 3.85
3226 4856 7.499438 TTATTTATCCGTTTTGATGCAAACG 57.501 32.000 13.17 13.17 32.79 3.60
3228 4858 9.227490 CGTATTATTTATCCGTTTTGATGCAAA 57.773 29.630 0.00 0.00 0.00 3.68
3229 4859 8.613482 TCGTATTATTTATCCGTTTTGATGCAA 58.387 29.630 0.00 0.00 0.00 4.08
3230 4860 8.065407 GTCGTATTATTTATCCGTTTTGATGCA 58.935 33.333 0.00 0.00 0.00 3.96
3231 4861 8.280497 AGTCGTATTATTTATCCGTTTTGATGC 58.720 33.333 0.00 0.00 0.00 3.91
3232 4862 9.793245 GAGTCGTATTATTTATCCGTTTTGATG 57.207 33.333 0.00 0.00 0.00 3.07
3233 4863 9.537192 TGAGTCGTATTATTTATCCGTTTTGAT 57.463 29.630 0.00 0.00 0.00 2.57
3234 4864 8.929827 TGAGTCGTATTATTTATCCGTTTTGA 57.070 30.769 0.00 0.00 0.00 2.69
3235 4865 9.417284 GTTGAGTCGTATTATTTATCCGTTTTG 57.583 33.333 0.00 0.00 0.00 2.44
3236 4866 8.323140 CGTTGAGTCGTATTATTTATCCGTTTT 58.677 33.333 0.00 0.00 0.00 2.43
3237 4867 7.515684 GCGTTGAGTCGTATTATTTATCCGTTT 60.516 37.037 0.00 0.00 0.00 3.60
3238 4868 6.074676 GCGTTGAGTCGTATTATTTATCCGTT 60.075 38.462 0.00 0.00 0.00 4.44
3239 4869 5.400485 GCGTTGAGTCGTATTATTTATCCGT 59.600 40.000 0.00 0.00 0.00 4.69
3240 4870 5.441099 CGCGTTGAGTCGTATTATTTATCCG 60.441 44.000 0.00 0.00 0.00 4.18
3241 4871 5.664735 GCGCGTTGAGTCGTATTATTTATCC 60.665 44.000 8.43 0.00 0.00 2.59
3242 4872 5.108141 TGCGCGTTGAGTCGTATTATTTATC 60.108 40.000 8.43 0.00 0.00 1.75
3243 4873 4.741185 TGCGCGTTGAGTCGTATTATTTAT 59.259 37.500 8.43 0.00 0.00 1.40
3244 4874 4.104066 TGCGCGTTGAGTCGTATTATTTA 58.896 39.130 8.43 0.00 0.00 1.40
3245 4875 2.924926 TGCGCGTTGAGTCGTATTATTT 59.075 40.909 8.43 0.00 0.00 1.40
3246 4876 2.532235 TGCGCGTTGAGTCGTATTATT 58.468 42.857 8.43 0.00 0.00 1.40
3247 4877 2.197792 TGCGCGTTGAGTCGTATTAT 57.802 45.000 8.43 0.00 0.00 1.28
3248 4878 1.650153 GTTGCGCGTTGAGTCGTATTA 59.350 47.619 8.43 0.00 0.00 0.98
3249 4879 0.437295 GTTGCGCGTTGAGTCGTATT 59.563 50.000 8.43 0.00 0.00 1.89
3250 4880 1.349259 GGTTGCGCGTTGAGTCGTAT 61.349 55.000 8.43 0.00 0.00 3.06
3251 4881 2.017783 GGTTGCGCGTTGAGTCGTA 61.018 57.895 8.43 0.00 0.00 3.43
3252 4882 3.335534 GGTTGCGCGTTGAGTCGT 61.336 61.111 8.43 0.00 0.00 4.34
3253 4883 4.409588 CGGTTGCGCGTTGAGTCG 62.410 66.667 8.43 0.95 0.00 4.18
3254 4884 4.719616 GCGGTTGCGCGTTGAGTC 62.720 66.667 8.43 0.00 0.00 3.36
3264 4894 5.389411 GGACAAAATTTAAGAATGCGGTTGC 60.389 40.000 0.00 0.00 43.20 4.17
3265 4895 5.120053 GGGACAAAATTTAAGAATGCGGTTG 59.880 40.000 0.00 0.00 0.00 3.77
3266 4896 5.011635 AGGGACAAAATTTAAGAATGCGGTT 59.988 36.000 0.00 0.00 0.00 4.44
3267 4897 4.526650 AGGGACAAAATTTAAGAATGCGGT 59.473 37.500 0.00 0.00 0.00 5.68
3268 4898 5.072040 AGGGACAAAATTTAAGAATGCGG 57.928 39.130 0.00 0.00 0.00 5.69
3269 4899 5.286082 CGAAGGGACAAAATTTAAGAATGCG 59.714 40.000 0.00 0.00 0.00 4.73
3270 4900 6.632171 CGAAGGGACAAAATTTAAGAATGC 57.368 37.500 0.00 0.00 0.00 3.56
3271 4901 6.792846 TGCCGAAGGGACAAAATTTAAGAATG 60.793 38.462 0.00 0.00 44.49 2.67
3272 4902 5.245075 TGCCGAAGGGACAAAATTTAAGAAT 59.755 36.000 0.00 0.00 44.49 2.40
3273 4903 4.585162 TGCCGAAGGGACAAAATTTAAGAA 59.415 37.500 0.00 0.00 44.49 2.52
3274 4904 4.145807 TGCCGAAGGGACAAAATTTAAGA 58.854 39.130 0.00 0.00 44.49 2.10
3275 4905 4.513198 TGCCGAAGGGACAAAATTTAAG 57.487 40.909 0.00 0.00 44.49 1.85
3295 4925 2.063541 GAAATTGGGCGAGCCGGATG 62.064 60.000 5.05 0.00 36.85 3.51
3296 4926 1.823899 GAAATTGGGCGAGCCGGAT 60.824 57.895 5.05 0.00 36.85 4.18
3297 4927 2.437716 GAAATTGGGCGAGCCGGA 60.438 61.111 5.05 0.00 36.85 5.14
3298 4928 3.518068 GGAAATTGGGCGAGCCGG 61.518 66.667 8.14 0.00 36.85 6.13
3299 4929 3.876198 CGGAAATTGGGCGAGCCG 61.876 66.667 8.14 0.00 36.85 5.52
3300 4930 3.518068 CCGGAAATTGGGCGAGCC 61.518 66.667 5.37 5.37 0.00 4.70
3301 4931 4.193334 GCCGGAAATTGGGCGAGC 62.193 66.667 5.05 0.00 39.93 5.03
3305 4935 3.581687 TTTGCGCCGGAAATTGGGC 62.582 57.895 5.05 0.00 45.95 5.36
3306 4936 1.736282 GTTTGCGCCGGAAATTGGG 60.736 57.895 5.05 0.00 0.00 4.12
3307 4937 0.389687 ATGTTTGCGCCGGAAATTGG 60.390 50.000 5.05 0.00 0.00 3.16
3308 4938 0.714994 CATGTTTGCGCCGGAAATTG 59.285 50.000 5.05 4.94 0.00 2.32
3309 4939 1.013524 GCATGTTTGCGCCGGAAATT 61.014 50.000 5.05 0.00 39.49 1.82
3310 4940 1.445926 GCATGTTTGCGCCGGAAAT 60.446 52.632 5.05 0.00 39.49 2.17
3311 4941 2.049618 GCATGTTTGCGCCGGAAA 60.050 55.556 5.05 0.00 39.49 3.13
3319 4949 0.717224 CAAATCTGGCGCATGTTTGC 59.283 50.000 10.83 0.00 45.78 3.68
3320 4950 0.717224 GCAAATCTGGCGCATGTTTG 59.283 50.000 10.83 15.02 33.98 2.93
3321 4951 3.126729 GCAAATCTGGCGCATGTTT 57.873 47.368 10.83 1.28 0.00 2.83
3322 4952 4.895854 GCAAATCTGGCGCATGTT 57.104 50.000 10.83 0.00 0.00 2.71
3329 4959 0.179156 CATGTGGTCGCAAATCTGGC 60.179 55.000 0.00 0.00 0.00 4.85
3330 4960 0.452987 CCATGTGGTCGCAAATCTGG 59.547 55.000 0.00 0.00 0.00 3.86
3331 4961 1.131126 GTCCATGTGGTCGCAAATCTG 59.869 52.381 0.00 0.00 36.34 2.90
3332 4962 1.453155 GTCCATGTGGTCGCAAATCT 58.547 50.000 0.00 0.00 36.34 2.40
3333 4963 0.096976 CGTCCATGTGGTCGCAAATC 59.903 55.000 5.81 0.00 39.56 2.17
3334 4964 2.170738 CGTCCATGTGGTCGCAAAT 58.829 52.632 5.81 0.00 39.56 2.32
3335 4965 3.649096 CGTCCATGTGGTCGCAAA 58.351 55.556 5.81 0.00 39.56 3.68
3340 4970 1.800315 CGACGACGTCCATGTGGTC 60.800 63.158 21.63 9.30 42.17 4.02
3341 4971 1.798234 TTCGACGACGTCCATGTGGT 61.798 55.000 21.63 0.00 40.69 4.16
3342 4972 1.081041 TTCGACGACGTCCATGTGG 60.081 57.895 21.63 7.16 40.69 4.17
3343 4973 1.661948 CGTTCGACGACGTCCATGTG 61.662 60.000 21.63 7.87 46.05 3.21
3344 4974 1.441515 CGTTCGACGACGTCCATGT 60.442 57.895 21.63 1.56 46.05 3.21
3345 4975 2.150218 CCGTTCGACGACGTCCATG 61.150 63.158 21.63 13.45 46.05 3.66
3346 4976 2.177531 CCGTTCGACGACGTCCAT 59.822 61.111 21.63 0.00 46.05 3.41
3347 4977 2.971959 TCCGTTCGACGACGTCCA 60.972 61.111 21.63 6.83 46.05 4.02
3348 4978 2.500582 GTCCGTTCGACGACGTCC 60.501 66.667 21.63 7.48 46.05 4.79
3355 4985 3.749373 CGTGCACGTCCGTTCGAC 61.749 66.667 30.50 0.00 38.21 4.20


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

AutoCloner maintained by Alex Coulton.