Multiple sequence alignment - TraesCS2D01G157600

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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 TraesCS2D01G157600 chr2D 100.000 4122 0 0 1 4122 100956124 100952003 0.000000e+00 7613.0
1 TraesCS2D01G157600 chr2D 89.615 2494 182 34 975 3439 100784410 100781965 0.000000e+00 3099.0
2 TraesCS2D01G157600 chr2D 88.721 2376 184 47 859 3208 101365385 101363068 0.000000e+00 2826.0
3 TraesCS2D01G157600 chr2D 89.950 1413 126 6 1773 3180 100420972 100422373 0.000000e+00 1808.0
4 TraesCS2D01G157600 chr2D 85.751 1172 159 7 1819 2988 101379049 101377884 0.000000e+00 1232.0
5 TraesCS2D01G157600 chr2D 91.966 697 43 10 1 692 150926551 150927239 0.000000e+00 965.0
6 TraesCS2D01G157600 chr2D 88.287 572 50 10 1152 1722 100420413 100420968 0.000000e+00 669.0
7 TraesCS2D01G157600 chr2D 86.598 582 47 19 1155 1720 101380187 101379621 7.570000e-172 614.0
8 TraesCS2D01G157600 chr2D 77.871 714 86 32 3203 3872 101308515 101307830 1.080000e-100 377.0
9 TraesCS2D01G157600 chr2B 88.830 2283 188 40 1068 3331 152472257 152474491 0.000000e+00 2741.0
10 TraesCS2D01G157600 chr2B 90.374 1122 73 14 975 2072 152571000 152569890 0.000000e+00 1441.0
11 TraesCS2D01G157600 chr2B 91.596 940 76 2 2183 3122 152569896 152568960 0.000000e+00 1295.0
12 TraesCS2D01G157600 chr2B 85.836 1172 158 7 1819 2988 152609756 152608591 0.000000e+00 1238.0
13 TraesCS2D01G157600 chr2B 86.243 567 63 10 1155 1720 152610646 152610094 5.900000e-168 601.0
14 TraesCS2D01G157600 chr2B 94.366 142 7 1 1 141 457383143 457383284 2.500000e-52 217.0
15 TraesCS2D01G157600 chr2A 90.315 2096 137 34 1055 3126 100633231 100631178 0.000000e+00 2686.0
16 TraesCS2D01G157600 chr2A 88.248 2238 188 42 1097 3316 100538339 100540519 0.000000e+00 2606.0
17 TraesCS2D01G157600 chr2A 88.175 1167 128 8 1823 2988 100651162 100650005 0.000000e+00 1382.0
18 TraesCS2D01G157600 chr2A 88.641 1030 89 17 2473 3485 100631171 100630153 0.000000e+00 1229.0
19 TraesCS2D01G157600 chr2A 92.114 634 41 7 228 858 38743122 38743749 0.000000e+00 885.0
20 TraesCS2D01G157600 chr2A 87.744 563 56 12 1158 1715 100656946 100656392 0.000000e+00 645.0
21 TraesCS2D01G157600 chr7B 94.077 861 42 7 1 857 683459346 683460201 0.000000e+00 1299.0
22 TraesCS2D01G157600 chr7B 95.070 142 6 1 1 141 642279600 642279459 5.360000e-54 222.0
23 TraesCS2D01G157600 chr7B 94.366 142 7 1 1 141 553815197 553815338 2.500000e-52 217.0
24 TraesCS2D01G157600 chr1A 93.056 864 46 11 1 857 518743876 518744732 0.000000e+00 1251.0
25 TraesCS2D01G157600 chr1A 92.958 142 9 1 1 141 426236709 426236568 5.400000e-49 206.0
26 TraesCS2D01G157600 chr7D 91.986 861 56 10 1 856 553080618 553079766 0.000000e+00 1195.0
27 TraesCS2D01G157600 chr3B 92.503 787 49 6 32 813 565572240 565571459 0.000000e+00 1118.0
28 TraesCS2D01G157600 chr3B 91.311 633 47 6 228 857 357765779 357765152 0.000000e+00 857.0
29 TraesCS2D01G157600 chr5A 91.943 633 42 7 228 857 678579047 678579673 0.000000e+00 878.0
30 TraesCS2D01G157600 chr1B 91.627 633 45 7 228 857 22893453 22892826 0.000000e+00 869.0
31 TraesCS2D01G157600 chr4A 84.444 810 121 4 2184 2989 714276993 714277801 0.000000e+00 793.0
32 TraesCS2D01G157600 chr4A 100.000 28 0 0 3808 3835 563832806 563832833 7.000000e-03 52.8


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 TraesCS2D01G157600 chr2D 100952003 100956124 4121 True 7613.0 7613 100.0000 1 4122 1 chr2D.!!$R2 4121
1 TraesCS2D01G157600 chr2D 100781965 100784410 2445 True 3099.0 3099 89.6150 975 3439 1 chr2D.!!$R1 2464
2 TraesCS2D01G157600 chr2D 101363068 101365385 2317 True 2826.0 2826 88.7210 859 3208 1 chr2D.!!$R4 2349
3 TraesCS2D01G157600 chr2D 100420413 100422373 1960 False 1238.5 1808 89.1185 1152 3180 2 chr2D.!!$F2 2028
4 TraesCS2D01G157600 chr2D 150926551 150927239 688 False 965.0 965 91.9660 1 692 1 chr2D.!!$F1 691
5 TraesCS2D01G157600 chr2D 101377884 101380187 2303 True 923.0 1232 86.1745 1155 2988 2 chr2D.!!$R5 1833
6 TraesCS2D01G157600 chr2D 101307830 101308515 685 True 377.0 377 77.8710 3203 3872 1 chr2D.!!$R3 669
7 TraesCS2D01G157600 chr2B 152472257 152474491 2234 False 2741.0 2741 88.8300 1068 3331 1 chr2B.!!$F1 2263
8 TraesCS2D01G157600 chr2B 152568960 152571000 2040 True 1368.0 1441 90.9850 975 3122 2 chr2B.!!$R1 2147
9 TraesCS2D01G157600 chr2B 152608591 152610646 2055 True 919.5 1238 86.0395 1155 2988 2 chr2B.!!$R2 1833
10 TraesCS2D01G157600 chr2A 100538339 100540519 2180 False 2606.0 2606 88.2480 1097 3316 1 chr2A.!!$F2 2219
11 TraesCS2D01G157600 chr2A 100630153 100633231 3078 True 1957.5 2686 89.4780 1055 3485 2 chr2A.!!$R3 2430
12 TraesCS2D01G157600 chr2A 100650005 100651162 1157 True 1382.0 1382 88.1750 1823 2988 1 chr2A.!!$R1 1165
13 TraesCS2D01G157600 chr2A 38743122 38743749 627 False 885.0 885 92.1140 228 858 1 chr2A.!!$F1 630
14 TraesCS2D01G157600 chr2A 100656392 100656946 554 True 645.0 645 87.7440 1158 1715 1 chr2A.!!$R2 557
15 TraesCS2D01G157600 chr7B 683459346 683460201 855 False 1299.0 1299 94.0770 1 857 1 chr7B.!!$F2 856
16 TraesCS2D01G157600 chr1A 518743876 518744732 856 False 1251.0 1251 93.0560 1 857 1 chr1A.!!$F1 856
17 TraesCS2D01G157600 chr7D 553079766 553080618 852 True 1195.0 1195 91.9860 1 856 1 chr7D.!!$R1 855
18 TraesCS2D01G157600 chr3B 565571459 565572240 781 True 1118.0 1118 92.5030 32 813 1 chr3B.!!$R2 781
19 TraesCS2D01G157600 chr3B 357765152 357765779 627 True 857.0 857 91.3110 228 857 1 chr3B.!!$R1 629
20 TraesCS2D01G157600 chr5A 678579047 678579673 626 False 878.0 878 91.9430 228 857 1 chr5A.!!$F1 629
21 TraesCS2D01G157600 chr1B 22892826 22893453 627 True 869.0 869 91.6270 228 857 1 chr1B.!!$R1 629
22 TraesCS2D01G157600 chr4A 714276993 714277801 808 False 793.0 793 84.4440 2184 2989 1 chr4A.!!$F2 805

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
962 986 0.165944 CCATGGTCAAAGCGAACGTC 59.834 55.0 2.57 0.0 32.01 4.34 F
2172 2748 0.041751 TTTATGTGTGTGTGTGCGCG 60.042 50.0 0.00 0.0 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2918 4154 0.179048 GCGTGATCACATCCATGGGA 60.179 55.0 24.93 0.68 45.56 4.37 R
4097 5383 0.250727 GGCCCACTTGAGCACAGTAA 60.251 55.0 0.00 0.00 0.00 2.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.787818 TCCCTGGAAAATATGTAATTACTTCCT 58.212 33.333 23.54 9.20 33.51 3.36
73 74 9.499479 AAATATATTTCAATGTGGTGTTGCAAA 57.501 25.926 0.00 0.00 0.00 3.68
420 427 9.971744 CCAAAATCGATTCCAATTATTTCAAAC 57.028 29.630 11.83 0.00 0.00 2.93
539 549 5.909621 AGATCACATGTTCAGGAATTTGG 57.090 39.130 0.00 0.00 0.00 3.28
794 809 5.013704 ACATGGTCCCACAACTTTAGATGTA 59.986 40.000 0.00 0.00 29.63 2.29
830 846 0.831307 GGGAAGATCACCGGTAGCTT 59.169 55.000 6.87 11.31 0.00 3.74
894 910 2.994995 TGATCTCACCCGCACCGT 60.995 61.111 0.00 0.00 0.00 4.83
916 932 3.455328 GGAACGCCTCTCTTAACCC 57.545 57.895 0.00 0.00 0.00 4.11
918 934 0.529378 GAACGCCTCTCTTAACCCGA 59.471 55.000 0.00 0.00 0.00 5.14
919 935 0.245813 AACGCCTCTCTTAACCCGAC 59.754 55.000 0.00 0.00 0.00 4.79
920 936 1.226603 CGCCTCTCTTAACCCGACG 60.227 63.158 0.00 0.00 0.00 5.12
921 937 1.888736 GCCTCTCTTAACCCGACGT 59.111 57.895 0.00 0.00 0.00 4.34
922 938 0.245813 GCCTCTCTTAACCCGACGTT 59.754 55.000 0.00 0.00 38.57 3.99
924 940 1.817447 CCTCTCTTAACCCGACGTTCT 59.183 52.381 0.00 0.00 35.79 3.01
926 942 2.228343 CTCTCTTAACCCGACGTTCTGT 59.772 50.000 0.00 0.00 35.79 3.41
927 943 3.411446 TCTCTTAACCCGACGTTCTGTA 58.589 45.455 0.00 0.00 35.79 2.74
957 981 1.377202 GAGGCCATGGTCAAAGCGA 60.377 57.895 20.74 0.00 0.00 4.93
959 983 1.212751 GGCCATGGTCAAAGCGAAC 59.787 57.895 12.68 0.00 0.00 3.95
960 984 1.154225 GCCATGGTCAAAGCGAACG 60.154 57.895 14.67 0.00 32.01 3.95
961 985 1.852067 GCCATGGTCAAAGCGAACGT 61.852 55.000 14.67 0.00 32.01 3.99
962 986 0.165944 CCATGGTCAAAGCGAACGTC 59.834 55.000 2.57 0.00 32.01 4.34
963 987 0.865111 CATGGTCAAAGCGAACGTCA 59.135 50.000 0.00 0.00 32.01 4.35
964 988 1.464608 CATGGTCAAAGCGAACGTCAT 59.535 47.619 0.00 0.00 32.01 3.06
966 990 2.967362 TGGTCAAAGCGAACGTCATAT 58.033 42.857 0.00 0.00 32.01 1.78
967 991 4.112716 TGGTCAAAGCGAACGTCATATA 57.887 40.909 0.00 0.00 32.01 0.86
968 992 4.496360 TGGTCAAAGCGAACGTCATATAA 58.504 39.130 0.00 0.00 32.01 0.98
969 993 4.930405 TGGTCAAAGCGAACGTCATATAAA 59.070 37.500 0.00 0.00 32.01 1.40
970 994 5.583061 TGGTCAAAGCGAACGTCATATAAAT 59.417 36.000 0.00 0.00 32.01 1.40
973 997 7.740346 GGTCAAAGCGAACGTCATATAAATATG 59.260 37.037 3.94 3.94 41.10 1.78
1025 1051 5.659440 ACAGAAACACACAAACATTTCCT 57.341 34.783 0.00 0.00 32.56 3.36
1039 1065 4.990526 ACATTTCCTGGTCTCATCAAACT 58.009 39.130 0.00 0.00 0.00 2.66
1043 1069 2.029020 TCCTGGTCTCATCAAACTCACG 60.029 50.000 0.00 0.00 0.00 4.35
1053 1079 1.060713 CAAACTCACGAGCAGTACCG 58.939 55.000 0.00 0.00 0.00 4.02
1077 1103 3.041211 AGCAGAGGCATACAATACAGGA 58.959 45.455 0.00 0.00 44.61 3.86
1113 1139 2.026822 TCCTTGTTCCTGAATCCTGAGC 60.027 50.000 0.00 0.00 0.00 4.26
1153 1188 0.325671 ATGGGTCTCGTCTGGATGGT 60.326 55.000 0.00 0.00 0.00 3.55
1423 1465 4.962155 ACGAAACTCAGACAATTCCTTCT 58.038 39.130 0.00 0.00 0.00 2.85
1424 1471 4.752101 ACGAAACTCAGACAATTCCTTCTG 59.248 41.667 0.00 2.92 40.65 3.02
1432 1479 5.190330 TCAGACAATTCCTTCTGATCCATGA 59.810 40.000 0.00 0.00 42.67 3.07
1433 1480 6.062749 CAGACAATTCCTTCTGATCCATGAT 58.937 40.000 0.00 0.00 41.65 2.45
1434 1481 7.071572 TCAGACAATTCCTTCTGATCCATGATA 59.928 37.037 0.00 0.00 42.67 2.15
1441 1488 6.138967 TCCTTCTGATCCATGATAGTCTTCA 58.861 40.000 0.00 0.00 0.00 3.02
1443 1490 6.705381 CCTTCTGATCCATGATAGTCTTCAAC 59.295 42.308 0.00 0.00 0.00 3.18
1454 1501 1.202758 AGTCTTCAACGCCATCACCAA 60.203 47.619 0.00 0.00 0.00 3.67
1463 1510 1.751437 GCCATCACCAACTAGTTCCC 58.249 55.000 4.77 0.00 0.00 3.97
1510 1570 1.282248 CGCACGTTCCTGTACTGGTG 61.282 60.000 17.42 10.06 0.00 4.17
1880 2446 1.153349 GATGTCGGAGTGGAAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
1916 2482 1.661341 GCAGCGTGGAGATTGATCTT 58.339 50.000 0.00 0.00 37.25 2.40
1997 2563 3.557686 GCTACGAACAGGGGAAAAAGGTA 60.558 47.826 0.00 0.00 0.00 3.08
2068 2634 1.067706 CGTGCAAATCCCAGCATTCAA 60.068 47.619 0.00 0.00 43.44 2.69
2099 2668 5.049336 GCAAGTTCTTCTTCTTCTTGTACCC 60.049 44.000 0.00 0.00 38.09 3.69
2119 2688 4.830600 ACCCTTGTCGGTTTAAATCAACAT 59.169 37.500 0.00 0.00 29.19 2.71
2126 2695 7.704271 TGTCGGTTTAAATCAACATACAACAA 58.296 30.769 0.00 0.00 0.00 2.83
2167 2743 9.897744 CAGAAATTAATCTTTATGTGTGTGTGT 57.102 29.630 0.00 0.00 0.00 3.72
2168 2744 9.897744 AGAAATTAATCTTTATGTGTGTGTGTG 57.102 29.630 0.00 0.00 0.00 3.82
2169 2745 8.519492 AAATTAATCTTTATGTGTGTGTGTGC 57.481 30.769 0.00 0.00 0.00 4.57
2170 2746 3.811722 ATCTTTATGTGTGTGTGTGCG 57.188 42.857 0.00 0.00 0.00 5.34
2171 2747 1.262950 TCTTTATGTGTGTGTGTGCGC 59.737 47.619 0.00 0.00 0.00 6.09
2172 2748 0.041751 TTTATGTGTGTGTGTGCGCG 60.042 50.000 0.00 0.00 0.00 6.86
2173 2749 2.436997 TTATGTGTGTGTGTGCGCGC 62.437 55.000 27.26 27.26 36.27 6.86
2282 2858 1.751349 AAAGCTGCCTTGCCACCAAG 61.751 55.000 0.00 0.00 46.38 3.61
2403 2982 2.550830 TGAGTGCAAGACCTTCTTCC 57.449 50.000 0.00 0.00 33.78 3.46
2547 3126 1.176527 CGGGGACATGCTCAACAAAT 58.823 50.000 0.00 0.00 0.00 2.32
2656 3235 0.675633 GTTGGTGGCATCAAAGTGCT 59.324 50.000 15.97 0.00 44.45 4.40
2764 3343 5.878406 ATAAGGTTCGAGAATGGAGTGAT 57.122 39.130 0.00 0.00 0.00 3.06
2771 3350 1.767681 GAGAATGGAGTGATGAGGGCT 59.232 52.381 0.00 0.00 0.00 5.19
2806 3385 3.011566 TGCCTTGTTGTCTTTCTCCAA 57.988 42.857 0.00 0.00 0.00 3.53
2822 3401 1.077501 CAATGGGCCGAGGTCATGT 60.078 57.895 0.00 0.00 0.00 3.21
2865 4101 1.300963 GAGGCCAAGGCTGTGATCA 59.699 57.895 5.01 0.00 38.98 2.92
2918 4154 3.719268 TCACCAAAGTATGTCCATGCT 57.281 42.857 0.00 0.00 35.21 3.79
3267 4512 3.993081 GCAGGATGAGAAAGATCCATACG 59.007 47.826 0.00 0.00 41.82 3.06
3282 4527 3.762288 TCCATACGACTCACTGCTACTTT 59.238 43.478 0.00 0.00 0.00 2.66
3479 4739 6.954232 TCATTTTTAGGACCGTTAAGGATCT 58.046 36.000 0.00 0.00 45.00 2.75
3511 4785 0.040514 CAAGATGTCGCCAAAACGCA 60.041 50.000 0.00 0.00 0.00 5.24
3530 4804 3.706373 AGGGACGAGCGCACCAAT 61.706 61.111 11.47 0.00 0.00 3.16
3564 4838 4.341235 GCATACCCATTTTAGAAGGTTCCC 59.659 45.833 0.00 0.00 33.70 3.97
3565 4839 3.468071 ACCCATTTTAGAAGGTTCCCC 57.532 47.619 0.00 0.00 0.00 4.81
3566 4840 2.291346 ACCCATTTTAGAAGGTTCCCCG 60.291 50.000 0.00 0.00 35.12 5.73
3567 4841 2.291346 CCCATTTTAGAAGGTTCCCCGT 60.291 50.000 0.00 0.00 35.12 5.28
3624 4901 8.467963 TTTTTCGTATTTTCCTACCTTTTCCT 57.532 30.769 0.00 0.00 0.00 3.36
3625 4902 8.467963 TTTTCGTATTTTCCTACCTTTTCCTT 57.532 30.769 0.00 0.00 0.00 3.36
3627 4904 8.467963 TTCGTATTTTCCTACCTTTTCCTTTT 57.532 30.769 0.00 0.00 0.00 2.27
3628 4905 8.467963 TCGTATTTTCCTACCTTTTCCTTTTT 57.532 30.769 0.00 0.00 0.00 1.94
3806 5092 3.726607 TGCATTTCTTTTGCGGTTTCAT 58.273 36.364 0.00 0.00 43.10 2.57
3808 5094 5.292765 TGCATTTCTTTTGCGGTTTCATAA 58.707 33.333 0.00 0.00 43.10 1.90
3811 5097 7.041508 TGCATTTCTTTTGCGGTTTCATAAAAT 60.042 29.630 0.00 0.00 43.10 1.82
3812 5098 7.268872 GCATTTCTTTTGCGGTTTCATAAAATG 59.731 33.333 0.00 0.00 0.00 2.32
3815 5101 7.401484 TCTTTTGCGGTTTCATAAAATGTTC 57.599 32.000 0.00 0.00 0.00 3.18
3816 5102 6.980978 TCTTTTGCGGTTTCATAAAATGTTCA 59.019 30.769 0.00 0.00 0.00 3.18
3817 5103 6.517914 TTTGCGGTTTCATAAAATGTTCAC 57.482 33.333 0.00 0.00 0.00 3.18
3892 5178 6.804534 TCAGTTTTTCAAAGTATGTTTGCG 57.195 33.333 0.00 0.00 0.00 4.85
3893 5179 5.231147 TCAGTTTTTCAAAGTATGTTTGCGC 59.769 36.000 0.00 0.00 0.00 6.09
3894 5180 5.231991 CAGTTTTTCAAAGTATGTTTGCGCT 59.768 36.000 9.73 0.00 0.00 5.92
3895 5181 5.810074 AGTTTTTCAAAGTATGTTTGCGCTT 59.190 32.000 9.73 0.00 0.00 4.68
3896 5182 6.312672 AGTTTTTCAAAGTATGTTTGCGCTTT 59.687 30.769 9.73 0.00 0.00 3.51
3897 5183 6.654793 TTTTCAAAGTATGTTTGCGCTTTT 57.345 29.167 9.73 0.00 0.00 2.27
3898 5184 7.757097 TTTTCAAAGTATGTTTGCGCTTTTA 57.243 28.000 9.73 0.00 0.00 1.52
3899 5185 6.984740 TTCAAAGTATGTTTGCGCTTTTAG 57.015 33.333 9.73 0.00 0.00 1.85
3900 5186 6.307031 TCAAAGTATGTTTGCGCTTTTAGA 57.693 33.333 9.73 0.00 0.00 2.10
3901 5187 6.730175 TCAAAGTATGTTTGCGCTTTTAGAA 58.270 32.000 9.73 0.00 0.00 2.10
3902 5188 7.197017 TCAAAGTATGTTTGCGCTTTTAGAAA 58.803 30.769 9.73 0.00 0.00 2.52
3903 5189 7.702772 TCAAAGTATGTTTGCGCTTTTAGAAAA 59.297 29.630 9.73 0.00 0.00 2.29
3904 5190 6.986424 AGTATGTTTGCGCTTTTAGAAAAC 57.014 33.333 9.73 9.62 0.00 2.43
3905 5191 6.735130 AGTATGTTTGCGCTTTTAGAAAACT 58.265 32.000 9.73 0.00 33.07 2.66
3906 5192 7.867752 AGTATGTTTGCGCTTTTAGAAAACTA 58.132 30.769 9.73 0.98 33.07 2.24
3907 5193 8.512138 AGTATGTTTGCGCTTTTAGAAAACTAT 58.488 29.630 9.73 7.88 33.07 2.12
3908 5194 7.796958 ATGTTTGCGCTTTTAGAAAACTATC 57.203 32.000 9.73 0.00 33.07 2.08
3909 5195 6.730175 TGTTTGCGCTTTTAGAAAACTATCA 58.270 32.000 9.73 0.00 33.07 2.15
3910 5196 7.197017 TGTTTGCGCTTTTAGAAAACTATCAA 58.803 30.769 9.73 0.00 33.07 2.57
3911 5197 7.702772 TGTTTGCGCTTTTAGAAAACTATCAAA 59.297 29.630 9.73 0.00 33.07 2.69
3912 5198 8.536407 GTTTGCGCTTTTAGAAAACTATCAAAA 58.464 29.630 9.73 0.00 0.00 2.44
3913 5199 8.635877 TTGCGCTTTTAGAAAACTATCAAAAA 57.364 26.923 9.73 0.00 0.00 1.94
3914 5200 8.810652 TGCGCTTTTAGAAAACTATCAAAAAT 57.189 26.923 9.73 0.00 0.00 1.82
3915 5201 9.255304 TGCGCTTTTAGAAAACTATCAAAAATT 57.745 25.926 9.73 0.00 0.00 1.82
3916 5202 9.727403 GCGCTTTTAGAAAACTATCAAAAATTC 57.273 29.630 0.00 0.00 0.00 2.17
3937 5223 9.859152 AAATTCAAAAATATTGGGGTTTCAAGA 57.141 25.926 0.00 0.00 0.00 3.02
3938 5224 9.506018 AATTCAAAAATATTGGGGTTTCAAGAG 57.494 29.630 0.00 0.00 0.00 2.85
3939 5225 7.847711 TCAAAAATATTGGGGTTTCAAGAGA 57.152 32.000 0.00 0.00 0.00 3.10
3940 5226 8.256356 TCAAAAATATTGGGGTTTCAAGAGAA 57.744 30.769 0.00 0.00 0.00 2.87
3941 5227 8.147704 TCAAAAATATTGGGGTTTCAAGAGAAC 58.852 33.333 0.00 0.00 32.39 3.01
3942 5228 6.605471 AAATATTGGGGTTTCAAGAGAACC 57.395 37.500 0.00 0.00 32.39 3.62
3943 5229 3.903530 ATTGGGGTTTCAAGAGAACCT 57.096 42.857 6.04 0.00 32.39 3.50
3944 5230 3.680777 TTGGGGTTTCAAGAGAACCTT 57.319 42.857 6.04 0.00 32.39 3.50
3945 5231 3.680777 TGGGGTTTCAAGAGAACCTTT 57.319 42.857 6.04 0.00 32.39 3.11
3946 5232 3.295973 TGGGGTTTCAAGAGAACCTTTG 58.704 45.455 6.04 0.00 32.39 2.77
3947 5233 2.035961 GGGGTTTCAAGAGAACCTTTGC 59.964 50.000 6.04 0.00 32.39 3.68
3948 5234 2.693074 GGGTTTCAAGAGAACCTTTGCA 59.307 45.455 6.04 0.00 32.39 4.08
3949 5235 3.132111 GGGTTTCAAGAGAACCTTTGCAA 59.868 43.478 0.00 0.00 32.39 4.08
3950 5236 4.382577 GGGTTTCAAGAGAACCTTTGCAAA 60.383 41.667 12.14 12.14 32.39 3.68
3951 5237 5.359756 GGTTTCAAGAGAACCTTTGCAAAT 58.640 37.500 13.23 0.00 32.39 2.32
3952 5238 5.817296 GGTTTCAAGAGAACCTTTGCAAATT 59.183 36.000 13.23 4.90 32.39 1.82
3953 5239 6.316140 GGTTTCAAGAGAACCTTTGCAAATTT 59.684 34.615 13.23 9.05 32.39 1.82
3954 5240 6.907206 TTCAAGAGAACCTTTGCAAATTTG 57.093 33.333 13.23 14.03 31.42 2.32
3955 5241 6.219417 TCAAGAGAACCTTTGCAAATTTGA 57.781 33.333 22.31 10.72 31.42 2.69
3956 5242 6.275335 TCAAGAGAACCTTTGCAAATTTGAG 58.725 36.000 22.31 10.07 31.42 3.02
3957 5243 6.096705 TCAAGAGAACCTTTGCAAATTTGAGA 59.903 34.615 22.31 6.11 31.42 3.27
3958 5244 6.469782 AGAGAACCTTTGCAAATTTGAGAA 57.530 33.333 22.31 13.17 0.00 2.87
3959 5245 6.877236 AGAGAACCTTTGCAAATTTGAGAAA 58.123 32.000 22.31 16.47 0.00 2.52
3960 5246 7.330262 AGAGAACCTTTGCAAATTTGAGAAAA 58.670 30.769 22.31 15.64 0.00 2.29
3961 5247 7.278646 AGAGAACCTTTGCAAATTTGAGAAAAC 59.721 33.333 22.31 3.44 0.00 2.43
3962 5248 6.316140 AGAACCTTTGCAAATTTGAGAAAACC 59.684 34.615 22.31 2.72 0.00 3.27
3963 5249 5.744171 ACCTTTGCAAATTTGAGAAAACCT 58.256 33.333 22.31 2.77 0.00 3.50
3964 5250 6.179756 ACCTTTGCAAATTTGAGAAAACCTT 58.820 32.000 22.31 2.27 0.00 3.50
3965 5251 6.658816 ACCTTTGCAAATTTGAGAAAACCTTT 59.341 30.769 22.31 0.82 0.00 3.11
3966 5252 7.148255 ACCTTTGCAAATTTGAGAAAACCTTTC 60.148 33.333 22.31 0.05 0.00 2.62
3967 5253 7.066163 CCTTTGCAAATTTGAGAAAACCTTTCT 59.934 33.333 22.31 1.32 0.00 2.52
3968 5254 6.907206 TGCAAATTTGAGAAAACCTTTCTG 57.093 33.333 22.31 0.00 0.00 3.02
3969 5255 6.405538 TGCAAATTTGAGAAAACCTTTCTGT 58.594 32.000 22.31 0.00 0.00 3.41
3970 5256 6.878389 TGCAAATTTGAGAAAACCTTTCTGTT 59.122 30.769 22.31 0.00 0.00 3.16
3971 5257 7.390162 TGCAAATTTGAGAAAACCTTTCTGTTT 59.610 29.630 22.31 1.20 40.05 2.83
3983 5269 7.667043 AACCTTTCTGTTTTCAAAAACTTCC 57.333 32.000 16.77 0.00 46.37 3.46
3984 5270 6.764379 ACCTTTCTGTTTTCAAAAACTTCCA 58.236 32.000 16.77 0.00 46.37 3.53
3985 5271 7.220740 ACCTTTCTGTTTTCAAAAACTTCCAA 58.779 30.769 16.77 6.39 46.37 3.53
3986 5272 7.717436 ACCTTTCTGTTTTCAAAAACTTCCAAA 59.283 29.630 16.77 10.18 46.37 3.28
3987 5273 8.563732 CCTTTCTGTTTTCAAAAACTTCCAAAA 58.436 29.630 16.77 9.98 46.37 2.44
3991 5277 9.890352 TCTGTTTTCAAAAACTTCCAAAATTTG 57.110 25.926 16.77 0.00 46.37 2.32
3992 5278 9.890352 CTGTTTTCAAAAACTTCCAAAATTTGA 57.110 25.926 16.77 0.00 46.37 2.69
3993 5279 9.670719 TGTTTTCAAAAACTTCCAAAATTTGAC 57.329 25.926 16.77 0.00 46.37 3.18
3994 5280 9.670719 GTTTTCAAAAACTTCCAAAATTTGACA 57.329 25.926 7.37 0.00 43.68 3.58
4002 5288 9.838975 AAACTTCCAAAATTTGACAAAATGTTC 57.161 25.926 7.37 0.00 36.11 3.18
4003 5289 8.791327 ACTTCCAAAATTTGACAAAATGTTCT 57.209 26.923 7.37 0.00 36.11 3.01
4004 5290 8.882736 ACTTCCAAAATTTGACAAAATGTTCTC 58.117 29.630 7.37 0.00 36.11 2.87
4005 5291 8.783833 TTCCAAAATTTGACAAAATGTTCTCA 57.216 26.923 7.37 0.00 36.11 3.27
4006 5292 8.961294 TCCAAAATTTGACAAAATGTTCTCAT 57.039 26.923 7.37 0.00 36.11 2.90
4007 5293 9.393512 TCCAAAATTTGACAAAATGTTCTCATT 57.606 25.926 7.37 0.00 44.94 2.57
4052 5338 2.304751 AAAATGGACTACGGTAGCGG 57.695 50.000 19.72 4.06 0.00 5.52
4053 5339 0.462789 AAATGGACTACGGTAGCGGG 59.537 55.000 19.72 13.02 0.00 6.13
4054 5340 0.685458 AATGGACTACGGTAGCGGGT 60.685 55.000 19.72 16.14 0.00 5.28
4055 5341 0.685458 ATGGACTACGGTAGCGGGTT 60.685 55.000 19.72 1.09 0.00 4.11
4056 5342 0.899717 TGGACTACGGTAGCGGGTTT 60.900 55.000 19.72 0.00 0.00 3.27
4057 5343 1.102978 GGACTACGGTAGCGGGTTTA 58.897 55.000 19.72 0.64 0.00 2.01
4058 5344 1.202302 GGACTACGGTAGCGGGTTTAC 60.202 57.143 19.72 7.90 0.00 2.01
4059 5345 1.745653 GACTACGGTAGCGGGTTTACT 59.254 52.381 19.72 0.00 0.00 2.24
4060 5346 2.943033 GACTACGGTAGCGGGTTTACTA 59.057 50.000 19.72 0.00 0.00 1.82
4061 5347 2.683362 ACTACGGTAGCGGGTTTACTAC 59.317 50.000 19.72 0.00 38.42 2.73
4062 5348 1.544724 ACGGTAGCGGGTTTACTACA 58.455 50.000 19.72 0.00 40.45 2.74
4063 5349 1.474077 ACGGTAGCGGGTTTACTACAG 59.526 52.381 19.72 0.00 40.45 2.74
4064 5350 1.474077 CGGTAGCGGGTTTACTACAGT 59.526 52.381 6.39 0.00 40.45 3.55
4065 5351 2.733227 CGGTAGCGGGTTTACTACAGTG 60.733 54.545 6.39 0.00 40.45 3.66
4066 5352 2.265683 GTAGCGGGTTTACTACAGTGC 58.734 52.381 0.00 0.00 38.88 4.40
4067 5353 0.682852 AGCGGGTTTACTACAGTGCA 59.317 50.000 0.00 0.00 0.00 4.57
4068 5354 1.278127 AGCGGGTTTACTACAGTGCAT 59.722 47.619 0.00 0.00 0.00 3.96
4069 5355 1.396996 GCGGGTTTACTACAGTGCATG 59.603 52.381 0.00 0.00 0.00 4.06
4070 5356 2.695359 CGGGTTTACTACAGTGCATGT 58.305 47.619 0.00 0.00 46.45 3.21
4071 5357 3.071479 CGGGTTTACTACAGTGCATGTT 58.929 45.455 7.02 0.00 39.96 2.71
4072 5358 3.124636 CGGGTTTACTACAGTGCATGTTC 59.875 47.826 7.02 0.00 39.96 3.18
4073 5359 3.439129 GGGTTTACTACAGTGCATGTTCC 59.561 47.826 7.02 0.00 39.96 3.62
4074 5360 3.439129 GGTTTACTACAGTGCATGTTCCC 59.561 47.826 7.02 0.00 39.96 3.97
4075 5361 2.665649 TACTACAGTGCATGTTCCCG 57.334 50.000 7.02 0.00 39.96 5.14
4076 5362 0.973632 ACTACAGTGCATGTTCCCGA 59.026 50.000 7.02 0.00 39.96 5.14
4077 5363 1.555075 ACTACAGTGCATGTTCCCGAT 59.445 47.619 7.02 0.00 39.96 4.18
4078 5364 2.027192 ACTACAGTGCATGTTCCCGATT 60.027 45.455 7.02 0.00 39.96 3.34
4079 5365 1.167851 ACAGTGCATGTTCCCGATTG 58.832 50.000 0.00 0.00 39.96 2.67
4080 5366 0.452987 CAGTGCATGTTCCCGATTGG 59.547 55.000 0.00 0.00 0.00 3.16
4081 5367 1.139520 GTGCATGTTCCCGATTGGC 59.860 57.895 0.00 0.00 0.00 4.52
4082 5368 1.001020 TGCATGTTCCCGATTGGCT 60.001 52.632 0.00 0.00 0.00 4.75
4083 5369 1.314534 TGCATGTTCCCGATTGGCTG 61.315 55.000 0.00 0.00 0.00 4.85
4084 5370 1.434696 CATGTTCCCGATTGGCTGC 59.565 57.895 0.00 0.00 0.00 5.25
4085 5371 1.001020 ATGTTCCCGATTGGCTGCA 60.001 52.632 0.50 0.00 0.00 4.41
4086 5372 1.033746 ATGTTCCCGATTGGCTGCAG 61.034 55.000 10.11 10.11 0.00 4.41
4087 5373 1.377202 GTTCCCGATTGGCTGCAGA 60.377 57.895 20.43 0.00 0.00 4.26
4088 5374 0.960364 GTTCCCGATTGGCTGCAGAA 60.960 55.000 20.43 3.67 0.00 3.02
4089 5375 0.677731 TTCCCGATTGGCTGCAGAAG 60.678 55.000 20.43 0.67 0.00 2.85
4101 5387 3.540314 CTGCAGAAGCCTGATCTTACT 57.460 47.619 8.42 0.00 43.02 2.24
4102 5388 3.196463 CTGCAGAAGCCTGATCTTACTG 58.804 50.000 8.42 0.00 43.02 2.74
4103 5389 2.568956 TGCAGAAGCCTGATCTTACTGT 59.431 45.455 0.00 0.00 43.02 3.55
4104 5390 2.935201 GCAGAAGCCTGATCTTACTGTG 59.065 50.000 0.00 0.00 43.02 3.66
4105 5391 2.935201 CAGAAGCCTGATCTTACTGTGC 59.065 50.000 0.00 0.00 43.02 4.57
4106 5392 2.836981 AGAAGCCTGATCTTACTGTGCT 59.163 45.455 0.00 0.00 0.00 4.40
4107 5393 2.977772 AGCCTGATCTTACTGTGCTC 57.022 50.000 0.00 0.00 0.00 4.26
4108 5394 2.182827 AGCCTGATCTTACTGTGCTCA 58.817 47.619 0.00 0.00 0.00 4.26
4109 5395 2.568956 AGCCTGATCTTACTGTGCTCAA 59.431 45.455 0.00 0.00 0.00 3.02
4110 5396 2.935201 GCCTGATCTTACTGTGCTCAAG 59.065 50.000 0.00 0.00 0.00 3.02
4111 5397 3.618507 GCCTGATCTTACTGTGCTCAAGT 60.619 47.826 0.00 0.00 0.00 3.16
4112 5398 3.931468 CCTGATCTTACTGTGCTCAAGTG 59.069 47.826 0.00 0.00 0.00 3.16
4113 5399 3.930336 TGATCTTACTGTGCTCAAGTGG 58.070 45.455 0.00 0.00 0.00 4.00
4114 5400 2.839486 TCTTACTGTGCTCAAGTGGG 57.161 50.000 0.00 0.00 0.00 4.61
4115 5401 1.160137 CTTACTGTGCTCAAGTGGGC 58.840 55.000 0.00 0.00 0.00 5.36
4116 5402 0.250727 TTACTGTGCTCAAGTGGGCC 60.251 55.000 0.00 0.00 0.00 5.80
4117 5403 1.414866 TACTGTGCTCAAGTGGGCCA 61.415 55.000 0.00 0.00 0.00 5.36
4118 5404 1.970114 CTGTGCTCAAGTGGGCCAG 60.970 63.158 6.40 4.18 0.00 4.85
4119 5405 2.113986 GTGCTCAAGTGGGCCAGT 59.886 61.111 6.40 7.51 0.00 4.00
4120 5406 1.968540 GTGCTCAAGTGGGCCAGTC 60.969 63.158 15.65 2.28 0.00 3.51
4121 5407 2.149383 TGCTCAAGTGGGCCAGTCT 61.149 57.895 15.65 1.85 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
494 504 9.750125 ATCTTTAGAACAAGACCAATTTTGAAC 57.250 29.630 0.00 0.00 35.57 3.18
516 526 6.012113 TCCAAATTCCTGAACATGTGATCTT 58.988 36.000 0.00 0.00 0.00 2.40
664 677 2.254546 TTGACAGAAACGGCACTCAT 57.745 45.000 0.00 0.00 0.00 2.90
665 678 2.031258 TTTGACAGAAACGGCACTCA 57.969 45.000 0.00 0.00 0.00 3.41
666 679 2.287009 CCTTTTGACAGAAACGGCACTC 60.287 50.000 0.00 0.00 0.00 3.51
667 680 1.676006 CCTTTTGACAGAAACGGCACT 59.324 47.619 0.00 0.00 0.00 4.40
794 809 0.395311 CCCATCAATGAGGTGCTGCT 60.395 55.000 0.00 0.00 0.00 4.24
894 910 1.068055 GTTAAGAGAGGCGTTCCGTCA 60.068 52.381 0.00 0.00 37.47 4.35
899 915 0.529378 TCGGGTTAAGAGAGGCGTTC 59.471 55.000 0.00 0.00 0.00 3.95
906 922 2.233271 ACAGAACGTCGGGTTAAGAGA 58.767 47.619 0.00 0.00 39.50 3.10
907 923 2.719426 ACAGAACGTCGGGTTAAGAG 57.281 50.000 0.00 0.00 39.50 2.85
908 924 2.228822 GGTACAGAACGTCGGGTTAAGA 59.771 50.000 0.00 0.00 39.50 2.10
909 925 2.599659 GGTACAGAACGTCGGGTTAAG 58.400 52.381 0.00 0.00 39.50 1.85
910 926 1.272212 GGGTACAGAACGTCGGGTTAA 59.728 52.381 0.00 0.00 39.50 2.01
911 927 0.887933 GGGTACAGAACGTCGGGTTA 59.112 55.000 0.00 0.00 39.50 2.85
912 928 1.667722 GGGTACAGAACGTCGGGTT 59.332 57.895 0.00 0.00 42.96 4.11
913 929 2.629656 CGGGTACAGAACGTCGGGT 61.630 63.158 0.00 0.00 0.00 5.28
916 932 2.505557 GCCGGGTACAGAACGTCG 60.506 66.667 2.18 0.00 0.00 5.12
918 934 2.985282 TCGCCGGGTACAGAACGT 60.985 61.111 2.18 0.00 0.00 3.99
919 935 2.505557 GTCGCCGGGTACAGAACG 60.506 66.667 2.18 0.00 0.00 3.95
920 936 2.125793 GGTCGCCGGGTACAGAAC 60.126 66.667 2.18 0.00 0.00 3.01
921 937 3.384532 GGGTCGCCGGGTACAGAA 61.385 66.667 2.18 0.00 0.00 3.02
962 986 8.097038 CGGGGAGGTGGATATCATATTTATATG 58.903 40.741 4.83 3.79 41.10 1.78
963 987 7.237679 CCGGGGAGGTGGATATCATATTTATAT 59.762 40.741 4.83 0.00 34.51 0.86
964 988 6.557253 CCGGGGAGGTGGATATCATATTTATA 59.443 42.308 4.83 0.00 34.51 0.98
966 990 4.719773 CCGGGGAGGTGGATATCATATTTA 59.280 45.833 4.83 0.00 34.51 1.40
967 991 3.523564 CCGGGGAGGTGGATATCATATTT 59.476 47.826 4.83 0.00 34.51 1.40
968 992 3.115390 CCGGGGAGGTGGATATCATATT 58.885 50.000 4.83 0.00 34.51 1.28
969 993 2.764269 CCGGGGAGGTGGATATCATAT 58.236 52.381 4.83 0.00 34.51 1.78
970 994 1.899887 GCCGGGGAGGTGGATATCATA 60.900 57.143 2.18 0.00 43.70 2.15
973 997 2.593956 GGCCGGGGAGGTGGATATC 61.594 68.421 2.18 0.00 43.70 1.63
1002 1028 6.405286 CCAGGAAATGTTTGTGTGTTTCTGTA 60.405 38.462 0.00 0.00 32.61 2.74
1025 1051 2.610479 GCTCGTGAGTTTGATGAGACCA 60.610 50.000 0.00 0.00 0.00 4.02
1039 1065 1.880894 CTTCCGGTACTGCTCGTGA 59.119 57.895 0.00 0.00 0.00 4.35
1043 1069 0.179124 CTCTGCTTCCGGTACTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
1053 1079 3.808728 TGTATTGTATGCCTCTGCTTCC 58.191 45.455 0.00 0.00 38.71 3.46
1077 1103 5.123979 GGAACAAGGAGAAAAATATCAGCGT 59.876 40.000 0.00 0.00 0.00 5.07
1180 1215 1.227292 TACACCAGCGCGTTGAACA 60.227 52.632 25.28 3.51 0.00 3.18
1423 1465 4.371786 GCGTTGAAGACTATCATGGATCA 58.628 43.478 0.00 0.00 0.00 2.92
1424 1471 3.743396 GGCGTTGAAGACTATCATGGATC 59.257 47.826 0.00 0.00 0.00 3.36
1432 1479 2.236146 TGGTGATGGCGTTGAAGACTAT 59.764 45.455 0.00 0.00 0.00 2.12
1433 1480 1.621317 TGGTGATGGCGTTGAAGACTA 59.379 47.619 0.00 0.00 0.00 2.59
1434 1481 0.396435 TGGTGATGGCGTTGAAGACT 59.604 50.000 0.00 0.00 0.00 3.24
1441 1488 2.423577 GAACTAGTTGGTGATGGCGTT 58.576 47.619 14.14 0.00 0.00 4.84
1443 1490 1.369625 GGAACTAGTTGGTGATGGCG 58.630 55.000 14.14 0.00 0.00 5.69
1454 1501 1.831580 ACGTAAGAGCGGGAACTAGT 58.168 50.000 0.00 0.00 43.62 2.57
1463 1510 1.618861 CAGACCAGAACGTAAGAGCG 58.381 55.000 0.00 0.00 43.62 5.03
1538 1598 1.828331 GCTTCACCGTGTTCACGTCC 61.828 60.000 20.93 2.70 0.00 4.79
1768 1829 2.440501 CATCGCGCACACTTAAAATCC 58.559 47.619 8.75 0.00 0.00 3.01
1916 2482 0.324943 GCTCCTCAAACTGGTGGCTA 59.675 55.000 0.00 0.00 0.00 3.93
2068 2634 8.348507 CAAGAAGAAGAAGAACTTGCATTTACT 58.651 33.333 0.00 0.00 39.13 2.24
2099 2668 7.858382 TGTTGTATGTTGATTTAAACCGACAAG 59.142 33.333 6.73 0.00 35.77 3.16
2119 2688 5.714047 TGCTGTGTGAAAATGTTTGTTGTA 58.286 33.333 0.00 0.00 0.00 2.41
2126 2695 8.891671 ATTAATTTCTGCTGTGTGAAAATGTT 57.108 26.923 0.00 0.00 36.06 2.71
2168 2744 2.005537 CCTGATTAATTGCGCGCGC 61.006 57.895 45.02 45.02 42.35 6.86
2169 2745 0.579630 TACCTGATTAATTGCGCGCG 59.420 50.000 28.44 28.44 0.00 6.86
2170 2746 1.333791 GGTACCTGATTAATTGCGCGC 60.334 52.381 27.26 27.26 0.00 6.86
2171 2747 2.210116 AGGTACCTGATTAATTGCGCG 58.790 47.619 15.42 0.00 0.00 6.86
2172 2748 3.003378 GGAAGGTACCTGATTAATTGCGC 59.997 47.826 17.14 0.00 0.00 6.09
2173 2749 4.196193 TGGAAGGTACCTGATTAATTGCG 58.804 43.478 17.14 0.00 0.00 4.85
2174 2750 5.163550 GGTTGGAAGGTACCTGATTAATTGC 60.164 44.000 17.14 3.39 0.00 3.56
2175 2751 5.065988 CGGTTGGAAGGTACCTGATTAATTG 59.934 44.000 17.14 0.00 32.08 2.32
2282 2858 2.189521 CCGTAGCCCATGGTGTCC 59.810 66.667 11.73 0.00 0.00 4.02
2403 2982 3.443045 GGTGTCATGCCCGGCAAG 61.443 66.667 18.00 12.92 43.62 4.01
2531 3110 2.991190 CTGCAATTTGTTGAGCATGTCC 59.009 45.455 0.00 0.00 36.28 4.02
2547 3126 1.337703 GAACATGTTGACCAGCTGCAA 59.662 47.619 17.58 5.34 0.00 4.08
2583 3162 0.529119 GACACAGGGGCGTATAACCG 60.529 60.000 0.00 0.00 0.00 4.44
2656 3235 0.179234 TGTCAAGACCGTGCCTTCAA 59.821 50.000 0.00 0.00 0.00 2.69
2764 3343 2.436109 GGTGCTTTCCAGCCCTCA 59.564 61.111 0.00 0.00 46.74 3.86
2771 3350 1.912763 GGCATTGGGGTGCTTTCCA 60.913 57.895 0.00 0.00 44.45 3.53
2806 3385 1.902508 CTATACATGACCTCGGCCCAT 59.097 52.381 0.00 0.00 0.00 4.00
2822 3401 4.854173 TCATTGCAAAGTTCTGCCCTATA 58.146 39.130 1.71 0.00 41.90 1.31
2865 4101 5.551233 TGAAAACCTCTGAAGAATCACGAT 58.449 37.500 0.00 0.00 0.00 3.73
2918 4154 0.179048 GCGTGATCACATCCATGGGA 60.179 55.000 24.93 0.68 45.56 4.37
3141 4385 7.917505 GTGGCTGATGGTAAGAAAAATCAATAG 59.082 37.037 0.00 0.00 0.00 1.73
3142 4386 7.147915 GGTGGCTGATGGTAAGAAAAATCAATA 60.148 37.037 0.00 0.00 0.00 1.90
3143 4387 6.351286 GGTGGCTGATGGTAAGAAAAATCAAT 60.351 38.462 0.00 0.00 0.00 2.57
3253 4498 4.440802 GCAGTGAGTCGTATGGATCTTTCT 60.441 45.833 0.00 0.00 0.00 2.52
3267 4512 5.948992 AAATGGAAAAGTAGCAGTGAGTC 57.051 39.130 0.00 0.00 0.00 3.36
3340 4585 7.915397 AGCAATAGCATTTATTTTAGAACACGG 59.085 33.333 0.00 0.00 45.49 4.94
3341 4586 8.841444 AGCAATAGCATTTATTTTAGAACACG 57.159 30.769 0.00 0.00 45.49 4.49
3373 4633 9.959749 TGAGTGACAAATTTGTAATTAGGTTTC 57.040 29.630 23.33 7.92 42.43 2.78
3409 4669 6.936335 TCAGCATAGAAAAATCAACAGACTCA 59.064 34.615 0.00 0.00 0.00 3.41
3479 4739 4.386867 GACATCTTGTCGTAGGGATTGA 57.613 45.455 0.00 0.00 37.67 2.57
3541 4815 5.515797 GGAACCTTCTAAAATGGGTATGC 57.484 43.478 0.00 0.00 0.00 3.14
3775 5061 8.945057 ACCGCAAAAGAAATGCAAATTTATATT 58.055 25.926 0.00 0.00 44.01 1.28
3777 5063 7.897575 ACCGCAAAAGAAATGCAAATTTATA 57.102 28.000 0.00 0.00 44.01 0.98
3779 5065 6.610741 AACCGCAAAAGAAATGCAAATTTA 57.389 29.167 0.00 0.00 44.01 1.40
3781 5067 5.065731 TGAAACCGCAAAAGAAATGCAAATT 59.934 32.000 0.00 0.00 44.01 1.82
3783 5069 3.935203 TGAAACCGCAAAAGAAATGCAAA 59.065 34.783 0.00 0.00 44.01 3.68
3786 5072 5.837586 TTATGAAACCGCAAAAGAAATGC 57.162 34.783 0.00 0.00 40.41 3.56
3787 5073 8.281893 ACATTTTATGAAACCGCAAAAGAAATG 58.718 29.630 0.00 0.00 37.02 2.32
3788 5074 8.376889 ACATTTTATGAAACCGCAAAAGAAAT 57.623 26.923 0.00 0.00 0.00 2.17
3789 5075 7.778470 ACATTTTATGAAACCGCAAAAGAAA 57.222 28.000 0.00 0.00 0.00 2.52
3792 5078 7.062848 GTGAACATTTTATGAAACCGCAAAAG 58.937 34.615 0.00 0.00 0.00 2.27
3866 5152 8.963130 CGCAAACATACTTTGAAAAACTGAATA 58.037 29.630 0.00 0.00 0.00 1.75
3867 5153 7.516627 GCGCAAACATACTTTGAAAAACTGAAT 60.517 33.333 0.30 0.00 0.00 2.57
3872 5158 5.635549 AGCGCAAACATACTTTGAAAAAC 57.364 34.783 11.47 0.00 0.00 2.43
3873 5159 6.654793 AAAGCGCAAACATACTTTGAAAAA 57.345 29.167 11.47 0.00 31.41 1.94
3874 5160 6.654793 AAAAGCGCAAACATACTTTGAAAA 57.345 29.167 11.47 0.00 32.88 2.29
3875 5161 7.197017 TCTAAAAGCGCAAACATACTTTGAAA 58.803 30.769 11.47 0.00 32.88 2.69
3876 5162 6.730175 TCTAAAAGCGCAAACATACTTTGAA 58.270 32.000 11.47 0.00 32.88 2.69
3877 5163 6.307031 TCTAAAAGCGCAAACATACTTTGA 57.693 33.333 11.47 0.00 32.88 2.69
3878 5164 6.984740 TTCTAAAAGCGCAAACATACTTTG 57.015 33.333 11.47 0.00 32.88 2.77
3879 5165 7.704899 AGTTTTCTAAAAGCGCAAACATACTTT 59.295 29.630 11.47 0.00 33.92 2.66
3880 5166 7.200455 AGTTTTCTAAAAGCGCAAACATACTT 58.800 30.769 11.47 0.00 31.06 2.24
3881 5167 6.735130 AGTTTTCTAAAAGCGCAAACATACT 58.265 32.000 11.47 0.00 31.06 2.12
3882 5168 6.986424 AGTTTTCTAAAAGCGCAAACATAC 57.014 33.333 11.47 0.00 31.06 2.39
3883 5169 8.508062 TGATAGTTTTCTAAAAGCGCAAACATA 58.492 29.630 11.47 4.84 35.90 2.29
3884 5170 7.367285 TGATAGTTTTCTAAAAGCGCAAACAT 58.633 30.769 11.47 6.11 35.90 2.71
3885 5171 6.730175 TGATAGTTTTCTAAAAGCGCAAACA 58.270 32.000 11.47 1.48 35.90 2.83
3886 5172 7.617533 TTGATAGTTTTCTAAAAGCGCAAAC 57.382 32.000 11.47 9.73 35.90 2.93
3887 5173 8.635877 TTTTGATAGTTTTCTAAAAGCGCAAA 57.364 26.923 11.47 0.00 35.90 3.68
3888 5174 8.635877 TTTTTGATAGTTTTCTAAAAGCGCAA 57.364 26.923 11.47 0.00 35.90 4.85
3889 5175 8.810652 ATTTTTGATAGTTTTCTAAAAGCGCA 57.189 26.923 11.47 0.00 35.10 6.09
3890 5176 9.727403 GAATTTTTGATAGTTTTCTAAAAGCGC 57.273 29.630 0.00 0.00 35.10 5.92
3911 5197 9.859152 TCTTGAAACCCCAATATTTTTGAATTT 57.141 25.926 0.00 0.00 0.00 1.82
3912 5198 9.506018 CTCTTGAAACCCCAATATTTTTGAATT 57.494 29.630 0.00 0.00 0.00 2.17
3913 5199 8.879227 TCTCTTGAAACCCCAATATTTTTGAAT 58.121 29.630 0.00 0.00 0.00 2.57
3914 5200 8.256356 TCTCTTGAAACCCCAATATTTTTGAA 57.744 30.769 0.00 0.00 0.00 2.69
3915 5201 7.847711 TCTCTTGAAACCCCAATATTTTTGA 57.152 32.000 0.00 0.00 0.00 2.69
3916 5202 7.387673 GGTTCTCTTGAAACCCCAATATTTTTG 59.612 37.037 0.00 0.00 33.97 2.44
3917 5203 7.292356 AGGTTCTCTTGAAACCCCAATATTTTT 59.708 33.333 1.53 0.00 40.62 1.94
3918 5204 6.787458 AGGTTCTCTTGAAACCCCAATATTTT 59.213 34.615 1.53 0.00 40.62 1.82
3919 5205 6.322931 AGGTTCTCTTGAAACCCCAATATTT 58.677 36.000 1.53 0.00 40.62 1.40
3920 5206 5.903923 AGGTTCTCTTGAAACCCCAATATT 58.096 37.500 1.53 0.00 40.62 1.28
3921 5207 5.536497 AGGTTCTCTTGAAACCCCAATAT 57.464 39.130 1.53 0.00 40.62 1.28
3922 5208 5.333566 AAGGTTCTCTTGAAACCCCAATA 57.666 39.130 1.53 0.00 40.62 1.90
3923 5209 3.903530 AGGTTCTCTTGAAACCCCAAT 57.096 42.857 1.53 0.00 40.62 3.16
3924 5210 3.680777 AAGGTTCTCTTGAAACCCCAA 57.319 42.857 1.53 0.00 40.62 4.12
3925 5211 3.295973 CAAAGGTTCTCTTGAAACCCCA 58.704 45.455 1.53 0.00 40.62 4.96
3926 5212 2.035961 GCAAAGGTTCTCTTGAAACCCC 59.964 50.000 1.53 0.00 40.62 4.95
3927 5213 2.693074 TGCAAAGGTTCTCTTGAAACCC 59.307 45.455 1.53 0.00 40.62 4.11
3928 5214 4.385358 TTGCAAAGGTTCTCTTGAAACC 57.615 40.909 0.00 0.00 40.62 3.27
3929 5215 6.908870 AATTTGCAAAGGTTCTCTTGAAAC 57.091 33.333 18.19 0.00 40.06 2.78
3930 5216 7.102346 TCAAATTTGCAAAGGTTCTCTTGAAA 58.898 30.769 18.19 0.00 35.55 2.69
3931 5217 6.638610 TCAAATTTGCAAAGGTTCTCTTGAA 58.361 32.000 18.19 0.00 35.55 2.69
3932 5218 6.096705 TCTCAAATTTGCAAAGGTTCTCTTGA 59.903 34.615 18.19 14.00 35.55 3.02
3933 5219 6.275335 TCTCAAATTTGCAAAGGTTCTCTTG 58.725 36.000 18.19 11.04 35.55 3.02
3934 5220 6.469782 TCTCAAATTTGCAAAGGTTCTCTT 57.530 33.333 18.19 2.02 37.28 2.85
3935 5221 6.469782 TTCTCAAATTTGCAAAGGTTCTCT 57.530 33.333 18.19 0.00 0.00 3.10
3936 5222 7.401860 GTTTTCTCAAATTTGCAAAGGTTCTC 58.598 34.615 18.19 0.00 0.00 2.87
3937 5223 6.316140 GGTTTTCTCAAATTTGCAAAGGTTCT 59.684 34.615 18.19 0.00 0.00 3.01
3938 5224 6.316140 AGGTTTTCTCAAATTTGCAAAGGTTC 59.684 34.615 18.19 1.25 0.00 3.62
3939 5225 6.179756 AGGTTTTCTCAAATTTGCAAAGGTT 58.820 32.000 18.19 11.14 0.00 3.50
3940 5226 5.744171 AGGTTTTCTCAAATTTGCAAAGGT 58.256 33.333 18.19 5.17 0.00 3.50
3941 5227 6.682423 AAGGTTTTCTCAAATTTGCAAAGG 57.318 33.333 18.19 9.68 0.00 3.11
3942 5228 7.906527 CAGAAAGGTTTTCTCAAATTTGCAAAG 59.093 33.333 18.19 6.20 0.00 2.77
3943 5229 7.390162 ACAGAAAGGTTTTCTCAAATTTGCAAA 59.610 29.630 15.44 15.44 0.00 3.68
3944 5230 6.878389 ACAGAAAGGTTTTCTCAAATTTGCAA 59.122 30.769 13.54 0.00 0.00 4.08
3945 5231 6.405538 ACAGAAAGGTTTTCTCAAATTTGCA 58.594 32.000 13.54 0.00 0.00 4.08
3946 5232 6.908870 ACAGAAAGGTTTTCTCAAATTTGC 57.091 33.333 13.54 0.00 0.00 3.68
3968 5254 9.670719 TGTCAAATTTTGGAAGTTTTTGAAAAC 57.329 25.926 9.18 10.55 46.54 2.43
3976 5262 9.838975 GAACATTTTGTCAAATTTTGGAAGTTT 57.161 25.926 9.18 0.00 29.41 2.66
3977 5263 9.230122 AGAACATTTTGTCAAATTTTGGAAGTT 57.770 25.926 9.18 5.40 29.41 2.66
3978 5264 8.791327 AGAACATTTTGTCAAATTTTGGAAGT 57.209 26.923 9.18 0.00 29.41 3.01
3979 5265 8.881743 TGAGAACATTTTGTCAAATTTTGGAAG 58.118 29.630 9.18 0.00 32.25 3.46
3980 5266 8.783833 TGAGAACATTTTGTCAAATTTTGGAA 57.216 26.923 9.18 0.72 32.25 3.53
3981 5267 8.961294 ATGAGAACATTTTGTCAAATTTTGGA 57.039 26.923 9.18 0.00 38.43 3.53
4032 5318 2.624636 CCGCTACCGTAGTCCATTTTT 58.375 47.619 7.40 0.00 0.00 1.94
4033 5319 1.134610 CCCGCTACCGTAGTCCATTTT 60.135 52.381 7.40 0.00 0.00 1.82
4034 5320 0.462789 CCCGCTACCGTAGTCCATTT 59.537 55.000 7.40 0.00 0.00 2.32
4035 5321 0.685458 ACCCGCTACCGTAGTCCATT 60.685 55.000 7.40 0.00 0.00 3.16
4036 5322 0.685458 AACCCGCTACCGTAGTCCAT 60.685 55.000 7.40 0.00 0.00 3.41
4037 5323 0.899717 AAACCCGCTACCGTAGTCCA 60.900 55.000 7.40 0.00 0.00 4.02
4038 5324 1.102978 TAAACCCGCTACCGTAGTCC 58.897 55.000 7.40 0.00 0.00 3.85
4039 5325 1.745653 AGTAAACCCGCTACCGTAGTC 59.254 52.381 7.40 0.00 0.00 2.59
4040 5326 1.839424 AGTAAACCCGCTACCGTAGT 58.161 50.000 7.40 0.00 0.00 2.73
4041 5327 2.682856 TGTAGTAAACCCGCTACCGTAG 59.317 50.000 0.76 0.76 37.39 3.51
4042 5328 2.682856 CTGTAGTAAACCCGCTACCGTA 59.317 50.000 0.00 0.00 37.39 4.02
4043 5329 1.474077 CTGTAGTAAACCCGCTACCGT 59.526 52.381 0.00 0.00 37.39 4.83
4044 5330 1.474077 ACTGTAGTAAACCCGCTACCG 59.526 52.381 0.00 0.00 37.39 4.02
4045 5331 2.884827 CACTGTAGTAAACCCGCTACC 58.115 52.381 0.00 0.00 37.39 3.18
4046 5332 2.265683 GCACTGTAGTAAACCCGCTAC 58.734 52.381 0.00 0.00 38.35 3.58
4047 5333 1.894466 TGCACTGTAGTAAACCCGCTA 59.106 47.619 0.00 0.00 0.00 4.26
4048 5334 0.682852 TGCACTGTAGTAAACCCGCT 59.317 50.000 0.00 0.00 0.00 5.52
4049 5335 1.396996 CATGCACTGTAGTAAACCCGC 59.603 52.381 0.00 0.00 0.00 6.13
4050 5336 2.695359 ACATGCACTGTAGTAAACCCG 58.305 47.619 0.00 0.00 35.91 5.28
4051 5337 3.439129 GGAACATGCACTGTAGTAAACCC 59.561 47.826 0.00 0.00 36.98 4.11
4052 5338 3.439129 GGGAACATGCACTGTAGTAAACC 59.561 47.826 0.00 0.00 36.98 3.27
4053 5339 3.124636 CGGGAACATGCACTGTAGTAAAC 59.875 47.826 0.00 0.00 36.98 2.01
4054 5340 3.007074 TCGGGAACATGCACTGTAGTAAA 59.993 43.478 0.00 0.00 36.98 2.01
4055 5341 2.563620 TCGGGAACATGCACTGTAGTAA 59.436 45.455 0.00 0.00 36.98 2.24
4056 5342 2.172679 TCGGGAACATGCACTGTAGTA 58.827 47.619 0.00 0.00 36.98 1.82
4057 5343 0.973632 TCGGGAACATGCACTGTAGT 59.026 50.000 0.00 0.00 36.98 2.73
4058 5344 2.315925 ATCGGGAACATGCACTGTAG 57.684 50.000 0.00 0.00 36.98 2.74
4059 5345 2.355197 CAATCGGGAACATGCACTGTA 58.645 47.619 0.00 0.00 36.98 2.74
4060 5346 1.167851 CAATCGGGAACATGCACTGT 58.832 50.000 0.00 0.00 40.84 3.55
4061 5347 0.452987 CCAATCGGGAACATGCACTG 59.547 55.000 0.00 0.00 40.01 3.66
4062 5348 1.315257 GCCAATCGGGAACATGCACT 61.315 55.000 0.00 0.00 40.01 4.40
4063 5349 1.139520 GCCAATCGGGAACATGCAC 59.860 57.895 0.00 0.00 40.01 4.57
4064 5350 1.001020 AGCCAATCGGGAACATGCA 60.001 52.632 0.00 0.00 40.01 3.96
4065 5351 1.434696 CAGCCAATCGGGAACATGC 59.565 57.895 0.00 0.00 40.01 4.06
4066 5352 1.314534 TGCAGCCAATCGGGAACATG 61.315 55.000 0.00 0.00 40.01 3.21
4067 5353 1.001020 TGCAGCCAATCGGGAACAT 60.001 52.632 0.00 0.00 40.01 2.71
4068 5354 1.675310 CTGCAGCCAATCGGGAACA 60.675 57.895 0.00 0.00 40.01 3.18
4069 5355 0.960364 TTCTGCAGCCAATCGGGAAC 60.960 55.000 9.47 0.00 40.01 3.62
4070 5356 0.677731 CTTCTGCAGCCAATCGGGAA 60.678 55.000 9.47 0.00 40.01 3.97
4071 5357 1.078214 CTTCTGCAGCCAATCGGGA 60.078 57.895 9.47 0.00 40.01 5.14
4072 5358 2.768492 GCTTCTGCAGCCAATCGGG 61.768 63.158 9.47 0.00 43.65 5.14
4073 5359 2.796651 GCTTCTGCAGCCAATCGG 59.203 61.111 9.47 0.00 43.65 4.18
4081 5367 3.196463 CAGTAAGATCAGGCTTCTGCAG 58.804 50.000 7.63 7.63 41.91 4.41
4082 5368 2.568956 ACAGTAAGATCAGGCTTCTGCA 59.431 45.455 0.00 0.00 41.91 4.41
4083 5369 2.935201 CACAGTAAGATCAGGCTTCTGC 59.065 50.000 0.00 0.00 38.36 4.26
4084 5370 2.935201 GCACAGTAAGATCAGGCTTCTG 59.065 50.000 0.00 0.00 39.78 3.02
4085 5371 2.836981 AGCACAGTAAGATCAGGCTTCT 59.163 45.455 0.00 0.00 0.00 2.85
4086 5372 3.194062 GAGCACAGTAAGATCAGGCTTC 58.806 50.000 0.00 0.00 0.00 3.86
4087 5373 2.568956 TGAGCACAGTAAGATCAGGCTT 59.431 45.455 0.00 0.00 0.00 4.35
4088 5374 2.182827 TGAGCACAGTAAGATCAGGCT 58.817 47.619 0.00 0.00 0.00 4.58
4089 5375 2.680312 TGAGCACAGTAAGATCAGGC 57.320 50.000 0.00 0.00 0.00 4.85
4090 5376 3.931468 CACTTGAGCACAGTAAGATCAGG 59.069 47.826 0.00 0.00 0.00 3.86
4091 5377 3.931468 CCACTTGAGCACAGTAAGATCAG 59.069 47.826 0.00 0.00 0.00 2.90
4092 5378 3.306989 CCCACTTGAGCACAGTAAGATCA 60.307 47.826 0.00 0.00 0.00 2.92
4093 5379 3.265791 CCCACTTGAGCACAGTAAGATC 58.734 50.000 0.00 0.00 0.00 2.75
4094 5380 2.616510 GCCCACTTGAGCACAGTAAGAT 60.617 50.000 0.00 0.00 0.00 2.40
4095 5381 1.270839 GCCCACTTGAGCACAGTAAGA 60.271 52.381 0.00 0.00 0.00 2.10
4096 5382 1.160137 GCCCACTTGAGCACAGTAAG 58.840 55.000 0.00 0.00 0.00 2.34
4097 5383 0.250727 GGCCCACTTGAGCACAGTAA 60.251 55.000 0.00 0.00 0.00 2.24
4098 5384 1.374947 GGCCCACTTGAGCACAGTA 59.625 57.895 0.00 0.00 0.00 2.74
4099 5385 2.113986 GGCCCACTTGAGCACAGT 59.886 61.111 0.00 0.00 0.00 3.55
4100 5386 1.970114 CTGGCCCACTTGAGCACAG 60.970 63.158 0.00 0.00 0.00 3.66
4101 5387 2.113774 CTGGCCCACTTGAGCACA 59.886 61.111 0.00 0.00 0.00 4.57
4102 5388 1.968540 GACTGGCCCACTTGAGCAC 60.969 63.158 0.00 0.00 0.00 4.40
4103 5389 2.149383 AGACTGGCCCACTTGAGCA 61.149 57.895 0.00 0.00 0.00 4.26
4104 5390 2.753029 AGACTGGCCCACTTGAGC 59.247 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.