Multiple sequence alignment - TraesCS1A01G234700

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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 TraesCS1A01G234700 chr1A 100.000 5048 0 0 1 5048 412221937 412226984 0.000000e+00 9323.0
1 TraesCS1A01G234700 chr1A 91.573 178 14 1 4794 4970 51692601 51692424 1.400000e-60 244.0
2 TraesCS1A01G234700 chr1D 95.345 4640 135 34 257 4837 326588316 326583699 0.000000e+00 7297.0
3 TraesCS1A01G234700 chr1D 96.018 226 8 1 4824 5048 326562586 326562361 2.870000e-97 366.0
4 TraesCS1A01G234700 chr1D 94.009 217 13 0 3 219 326588826 326588610 3.770000e-86 329.0
5 TraesCS1A01G234700 chr1B 93.666 2684 115 32 456 3103 440505556 440502892 0.000000e+00 3964.0
6 TraesCS1A01G234700 chr1B 94.156 1369 75 5 3351 4717 440502220 440500855 0.000000e+00 2080.0
7 TraesCS1A01G234700 chr1B 92.308 221 16 1 3 223 440518659 440518440 3.790000e-81 313.0
8 TraesCS1A01G234700 chr1B 94.059 202 10 1 257 458 440518155 440517956 6.350000e-79 305.0
9 TraesCS1A01G234700 chr1B 91.228 171 13 1 3101 3269 440502405 440502235 1.090000e-56 231.0
10 TraesCS1A01G234700 chr1B 94.167 120 7 0 96 215 390268762 390268643 3.100000e-42 183.0
11 TraesCS1A01G234700 chr5D 88.796 357 30 6 4361 4717 452679873 452680219 3.610000e-116 429.0
12 TraesCS1A01G234700 chr5D 92.683 123 9 0 98 220 519276022 519276144 1.440000e-40 178.0
13 TraesCS1A01G234700 chr5D 89.130 92 9 1 1 92 37636998 37636908 4.130000e-21 113.0
14 TraesCS1A01G234700 chr5B 88.142 253 25 4 4361 4609 553181398 553181649 3.820000e-76 296.0
15 TraesCS1A01G234700 chr5B 83.708 178 22 6 96 266 516539242 516539419 1.450000e-35 161.0
16 TraesCS1A01G234700 chr7A 91.011 178 15 1 4794 4970 447758035 447757858 6.530000e-59 239.0
17 TraesCS1A01G234700 chr7A 90.449 178 16 1 4794 4970 359268948 359269125 3.040000e-57 233.0
18 TraesCS1A01G234700 chr7A 86.957 92 11 1 1 92 77483001 77483091 8.940000e-18 102.0
19 TraesCS1A01G234700 chr5A 88.202 178 20 1 4794 4970 57055779 57055602 1.420000e-50 211.0
20 TraesCS1A01G234700 chr7B 92.063 126 9 1 98 223 162843937 162843813 5.190000e-40 176.0
21 TraesCS1A01G234700 chr2A 90.769 130 12 0 98 227 686176520 686176391 1.870000e-39 174.0
22 TraesCS1A01G234700 chr3D 90.698 129 12 0 96 224 612265139 612265011 6.720000e-39 172.0
23 TraesCS1A01G234700 chr3D 84.706 170 17 7 98 264 25580729 25580566 1.450000e-35 161.0
24 TraesCS1A01G234700 chr3D 89.130 92 10 0 1 92 570541784 570541693 1.150000e-21 115.0
25 TraesCS1A01G234700 chr3A 89.130 92 10 0 1 92 744673740 744673649 1.150000e-21 115.0
26 TraesCS1A01G234700 chr4A 89.130 92 9 1 1 92 647262052 647261962 4.130000e-21 113.0
27 TraesCS1A01G234700 chr4A 86.957 92 11 1 1 92 647266672 647266582 8.940000e-18 102.0
28 TraesCS1A01G234700 chr6B 85.417 96 10 1 1 92 648845014 648845109 4.160000e-16 97.1


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 TraesCS1A01G234700 chr1A 412221937 412226984 5047 False 9323.000000 9323 100.000000 1 5048 1 chr1A.!!$F1 5047
1 TraesCS1A01G234700 chr1D 326583699 326588826 5127 True 3813.000000 7297 94.677000 3 4837 2 chr1D.!!$R2 4834
2 TraesCS1A01G234700 chr1B 440500855 440505556 4701 True 2091.666667 3964 93.016667 456 4717 3 chr1B.!!$R2 4261
3 TraesCS1A01G234700 chr1B 440517956 440518659 703 True 309.000000 313 93.183500 3 458 2 chr1B.!!$R3 455

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
869 1129 0.033011 ATACGTCCCTCCAGAGCTGT 60.033 55.000 0.0 0.0 0.00 4.40 F
906 1178 1.271762 ACGGGTCTAGCTATATCGCCA 60.272 52.381 0.0 0.0 0.00 5.69 F
1944 2273 1.243342 TGCCCGATGTGAAAGCTTGG 61.243 55.000 0.0 0.0 0.00 3.61 F
3807 4642 0.669318 TTGGTCGTGATGGAACGCTC 60.669 55.000 0.0 0.0 43.26 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2253 0.597568 CAAGCTTTCACATCGGGCAA 59.402 50.0 0.0 0.0 0.0 4.52 R
2801 3133 2.799126 AATGGTATTTGCGGAGGACA 57.201 45.0 0.0 0.0 0.0 4.02 R
3909 4744 0.523072 CCAACACGGCTTCATTCAGG 59.477 55.0 0.0 0.0 0.0 3.86 R
4995 5832 0.178924 AAGCAAGTTTGGGGCAGGAT 60.179 50.0 0.0 0.0 0.0 3.24 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
137 138 3.798515 TGGTTAGAGGGACAGTGGTATT 58.201 45.455 0.00 0.00 0.00 1.89
182 183 1.209261 TGGTGCTCGCATTATTCCTGA 59.791 47.619 0.00 0.00 0.00 3.86
191 192 8.196771 TGCTCGCATTATTCCTGAATTTATTTT 58.803 29.630 0.00 0.00 32.50 1.82
215 216 4.031028 GGATTTTCGATGATGTGCTTTCG 58.969 43.478 0.00 0.00 0.00 3.46
220 221 1.737838 GATGATGTGCTTTCGGTGGA 58.262 50.000 0.00 0.00 0.00 4.02
223 224 1.071542 TGATGTGCTTTCGGTGGAAGA 59.928 47.619 0.00 0.00 32.80 2.87
322 582 6.877322 AGGCGTGTGAGTAGTAATTGTTAAAT 59.123 34.615 0.00 0.00 0.00 1.40
402 662 8.632906 AAGAGAATGATCTTCTTCAACATTGT 57.367 30.769 8.29 0.00 34.37 2.71
403 663 9.730705 AAGAGAATGATCTTCTTCAACATTGTA 57.269 29.630 8.29 0.00 34.37 2.41
639 899 8.798859 ACAGATATAGTCAAAGATTTTGCAGT 57.201 30.769 0.00 0.00 0.00 4.40
652 912 7.516198 AGATTTTGCAGTAGAGACACAATTT 57.484 32.000 0.00 0.00 0.00 1.82
756 1016 2.430382 GAAGGAAGCCGACGTGACCA 62.430 60.000 0.00 0.00 0.00 4.02
778 1038 4.023707 CACCAATTCCTCATAAATCCTCGC 60.024 45.833 0.00 0.00 0.00 5.03
810 1070 1.491668 TGCCTATTTAGTCCTCGCCA 58.508 50.000 0.00 0.00 0.00 5.69
830 1090 0.454600 CATTCTCCGCTTGCAGCATT 59.545 50.000 0.00 0.00 42.58 3.56
869 1129 0.033011 ATACGTCCCTCCAGAGCTGT 60.033 55.000 0.00 0.00 0.00 4.40
897 1169 2.912987 ATCGCCTCACGGGTCTAGCT 62.913 60.000 0.00 0.00 43.89 3.32
906 1178 1.271762 ACGGGTCTAGCTATATCGCCA 60.272 52.381 0.00 0.00 0.00 5.69
1265 1567 1.378646 TCGACTCGCTCCCAGATGT 60.379 57.895 0.00 0.00 0.00 3.06
1369 1671 4.152938 TCTCAGTTTGCAGAATCGTGATTG 59.847 41.667 0.00 0.00 0.00 2.67
1370 1672 3.814842 TCAGTTTGCAGAATCGTGATTGT 59.185 39.130 0.00 0.00 0.00 2.71
1381 1710 8.551205 GCAGAATCGTGATTGTCATCTTATTAA 58.449 33.333 0.00 0.00 0.00 1.40
1413 1742 2.357637 GCAACTGGCTGACAAGTTTACA 59.642 45.455 0.00 0.00 40.25 2.41
1428 1757 8.370266 ACAAGTTTACAGTATATACCCTGTCA 57.630 34.615 9.32 0.00 40.90 3.58
1444 1773 5.175859 CCCTGTCATACAATTGTCTTACGT 58.824 41.667 15.85 0.00 0.00 3.57
1661 1990 6.070951 TCTGCTTCCCTACTAGTTAGTGTA 57.929 41.667 0.00 0.00 37.10 2.90
1823 2152 3.393426 ACCTCTGGGTCCTTAATACGA 57.607 47.619 0.00 0.00 43.38 3.43
1861 2190 6.560253 TTCAATTGAAGAGGCTGTAAGTTC 57.440 37.500 16.91 0.00 35.30 3.01
1862 2191 5.620206 TCAATTGAAGAGGCTGTAAGTTCA 58.380 37.500 5.45 0.00 35.30 3.18
1863 2192 6.061441 TCAATTGAAGAGGCTGTAAGTTCAA 58.939 36.000 5.45 0.00 38.84 2.69
1924 2253 4.021807 TGCATGCATTCAGTTTGAGTGATT 60.022 37.500 18.46 0.00 36.36 2.57
1944 2273 1.243342 TGCCCGATGTGAAAGCTTGG 61.243 55.000 0.00 0.00 0.00 3.61
1997 2326 4.852134 TTTCTTACGTGGTGCACTAGTA 57.148 40.909 17.98 14.88 31.34 1.82
2054 2383 3.949754 CACATATCAGGCCTTGTGATGTT 59.050 43.478 25.01 7.07 41.50 2.71
2119 2448 9.820229 CATCACAATAGTTTATGTTAACAACGT 57.180 29.630 13.23 0.00 0.00 3.99
2166 2495 5.227152 CCTGTTGTTTGGCAGGTTTATTAC 58.773 41.667 2.66 0.00 45.28 1.89
2174 2503 6.909550 TTGGCAGGTTTATTACTGTGAATT 57.090 33.333 0.00 0.00 37.07 2.17
2315 2644 3.720002 ACCCTGGTTCCTTTTACTTCTGA 59.280 43.478 0.00 0.00 0.00 3.27
2801 3133 1.455822 TGTGGAATGGGGGAGTTTCT 58.544 50.000 0.00 0.00 0.00 2.52
2833 3165 7.174946 CCGCAAATACCATTAACTCCTTATGAT 59.825 37.037 0.00 0.00 0.00 2.45
2857 3189 4.785346 ATGCTTCCATAATGAGACACCT 57.215 40.909 0.00 0.00 0.00 4.00
2972 3305 6.544564 GGGTTTTGAGAAAATGATATCGGGTA 59.455 38.462 0.00 0.00 32.22 3.69
3214 4038 7.459795 TGCTTACAATGGTGTTTCATATTCA 57.540 32.000 0.00 0.00 39.30 2.57
3269 4093 4.288398 TGTCCACCGAGGGTTGTTATATA 58.712 43.478 0.00 0.00 38.24 0.86
3270 4094 4.099881 TGTCCACCGAGGGTTGTTATATAC 59.900 45.833 0.00 0.00 38.24 1.47
3271 4095 4.343239 GTCCACCGAGGGTTGTTATATACT 59.657 45.833 0.00 0.00 38.24 2.12
3338 4172 6.918022 GCGTCTATTTTAATGGGATTTCTTGG 59.082 38.462 0.00 0.00 0.00 3.61
3353 4187 6.695713 GGATTTCTTGGTCAAGTTTTGTACAC 59.304 38.462 10.10 0.00 39.38 2.90
3404 4239 6.377327 TTTGTCTGATTTCCTCAACAGAAC 57.623 37.500 0.00 0.00 40.30 3.01
3444 4279 6.899393 TGCACTTCCTCAACAGAAAATAAT 57.101 33.333 0.00 0.00 0.00 1.28
3523 4358 3.573538 CACTCCATGTCTAGCTGCTATCT 59.426 47.826 10.23 0.00 0.00 1.98
3643 4478 4.783764 AAAAATGTTCGATGGTCCTTCC 57.216 40.909 0.00 0.00 0.00 3.46
3732 4567 2.614779 CAGAGAGTGTGCGACATCATT 58.385 47.619 0.00 0.00 0.00 2.57
3780 4615 4.171005 CAGCTGGAATTGTTGCAATACTG 58.829 43.478 5.57 0.00 0.00 2.74
3807 4642 0.669318 TTGGTCGTGATGGAACGCTC 60.669 55.000 0.00 0.00 43.26 5.03
3813 4648 1.021390 GTGATGGAACGCTCTGTGGG 61.021 60.000 0.00 0.00 0.00 4.61
3984 4819 0.696501 TTAAAGTGGTGGAGGAGGGC 59.303 55.000 0.00 0.00 0.00 5.19
4091 4926 3.256383 TGTGCACATGAAAAAGATGGAGG 59.744 43.478 17.42 0.00 0.00 4.30
4092 4927 2.827322 TGCACATGAAAAAGATGGAGGG 59.173 45.455 0.00 0.00 0.00 4.30
4107 4942 3.189606 TGGAGGGGTGTTCATTCATACT 58.810 45.455 0.00 0.00 0.00 2.12
4108 4943 3.054434 TGGAGGGGTGTTCATTCATACTG 60.054 47.826 0.00 0.00 0.00 2.74
4171 5006 8.344098 CGTAGGTATTTAGTTTGGTTTTGAACA 58.656 33.333 0.00 0.00 0.00 3.18
4263 5098 3.064931 GGTTCTTGTGTAGTCCCTTTCG 58.935 50.000 0.00 0.00 0.00 3.46
4275 5110 2.928116 GTCCCTTTCGGATGTTAAGTCG 59.072 50.000 0.00 0.00 44.66 4.18
4439 5275 4.818005 TCTCTATGTTGCAATGGTATGCTG 59.182 41.667 0.59 0.00 46.54 4.41
4451 5287 2.224646 TGGTATGCTGTGTGCCAGTTTA 60.225 45.455 0.00 0.00 43.55 2.01
4593 5429 1.213537 CAAATTGAGGCCGGCTGTG 59.786 57.895 28.56 7.50 0.00 3.66
4596 5432 2.410322 AATTGAGGCCGGCTGTGACA 62.410 55.000 28.56 15.87 0.00 3.58
4638 5474 4.335315 TGCTGAACAAAACTAGGTCACAAG 59.665 41.667 0.00 0.00 0.00 3.16
4680 5516 2.293122 ACTGCAGCAAATTCAGCGTTTA 59.707 40.909 15.27 0.00 37.01 2.01
4730 5566 2.726821 CAGGTACCCTGTGCATCAAAT 58.273 47.619 8.74 0.00 45.82 2.32
4814 5651 0.462047 CGGGTCGAAAGGAATCCCAG 60.462 60.000 5.91 0.00 38.15 4.45
4837 5674 2.811317 GCGAGGTTCCAGAGCGTG 60.811 66.667 0.00 0.00 0.00 5.34
4838 5675 2.962569 CGAGGTTCCAGAGCGTGA 59.037 61.111 0.00 0.00 0.00 4.35
4839 5676 1.513158 CGAGGTTCCAGAGCGTGAT 59.487 57.895 0.00 0.00 0.00 3.06
4840 5677 0.526524 CGAGGTTCCAGAGCGTGATC 60.527 60.000 0.00 0.00 0.00 2.92
4841 5678 0.820871 GAGGTTCCAGAGCGTGATCT 59.179 55.000 0.00 0.00 0.00 2.75
4842 5679 0.820871 AGGTTCCAGAGCGTGATCTC 59.179 55.000 0.00 0.00 0.00 2.75
4843 5680 0.179097 GGTTCCAGAGCGTGATCTCC 60.179 60.000 0.00 0.00 33.66 3.71
4844 5681 0.820871 GTTCCAGAGCGTGATCTCCT 59.179 55.000 0.00 0.00 33.66 3.69
4845 5682 1.107114 TTCCAGAGCGTGATCTCCTC 58.893 55.000 0.00 0.11 33.66 3.71
4846 5683 0.257328 TCCAGAGCGTGATCTCCTCT 59.743 55.000 8.91 8.91 36.43 3.69
4847 5684 0.667993 CCAGAGCGTGATCTCCTCTC 59.332 60.000 10.84 7.72 33.89 3.20
4848 5685 1.679139 CAGAGCGTGATCTCCTCTCT 58.321 55.000 10.84 9.36 33.89 3.10
4849 5686 2.023673 CAGAGCGTGATCTCCTCTCTT 58.976 52.381 10.84 0.00 33.89 2.85
4850 5687 3.210227 CAGAGCGTGATCTCCTCTCTTA 58.790 50.000 10.84 0.00 33.89 2.10
4851 5688 3.629855 CAGAGCGTGATCTCCTCTCTTAA 59.370 47.826 10.84 0.00 33.89 1.85
4852 5689 4.278170 CAGAGCGTGATCTCCTCTCTTAAT 59.722 45.833 10.84 0.00 33.89 1.40
4853 5690 4.518970 AGAGCGTGATCTCCTCTCTTAATC 59.481 45.833 8.91 0.00 30.46 1.75
4854 5691 3.252215 AGCGTGATCTCCTCTCTTAATCG 59.748 47.826 0.00 0.00 0.00 3.34
4855 5692 3.560503 CGTGATCTCCTCTCTTAATCGC 58.439 50.000 0.00 0.00 0.00 4.58
4856 5693 3.560503 GTGATCTCCTCTCTTAATCGCG 58.439 50.000 0.00 0.00 0.00 5.87
4857 5694 3.003897 GTGATCTCCTCTCTTAATCGCGT 59.996 47.826 5.77 0.00 0.00 6.01
4858 5695 3.003793 TGATCTCCTCTCTTAATCGCGTG 59.996 47.826 5.77 0.00 0.00 5.34
4859 5696 2.640184 TCTCCTCTCTTAATCGCGTGA 58.360 47.619 5.77 0.00 0.00 4.35
4860 5697 2.355132 TCTCCTCTCTTAATCGCGTGAC 59.645 50.000 5.77 0.00 0.00 3.67
4861 5698 1.063616 TCCTCTCTTAATCGCGTGACG 59.936 52.381 5.77 0.00 45.62 4.35
4874 5711 3.820160 GCGTGACGAAATAGTCTAAGC 57.180 47.619 10.10 0.00 41.47 3.09
4875 5712 3.436496 GCGTGACGAAATAGTCTAAGCT 58.564 45.455 10.10 0.00 41.47 3.74
4876 5713 3.482833 GCGTGACGAAATAGTCTAAGCTC 59.517 47.826 10.10 0.00 41.47 4.09
4877 5714 4.659088 CGTGACGAAATAGTCTAAGCTCA 58.341 43.478 0.00 0.00 41.47 4.26
4878 5715 5.274718 CGTGACGAAATAGTCTAAGCTCAT 58.725 41.667 0.00 0.00 41.47 2.90
4879 5716 6.427974 CGTGACGAAATAGTCTAAGCTCATA 58.572 40.000 0.00 0.00 41.47 2.15
4880 5717 6.575572 CGTGACGAAATAGTCTAAGCTCATAG 59.424 42.308 0.00 0.00 41.47 2.23
4881 5718 6.361214 GTGACGAAATAGTCTAAGCTCATAGC 59.639 42.308 0.00 0.00 40.64 2.97
4882 5719 6.263392 TGACGAAATAGTCTAAGCTCATAGCT 59.737 38.462 0.00 0.00 46.62 3.32
4897 5734 3.567473 GCTTCCTGCTGGAACGTC 58.433 61.111 20.15 9.31 46.57 4.34
4898 5735 2.035442 GCTTCCTGCTGGAACGTCC 61.035 63.158 20.15 6.43 46.57 4.79
4899 5736 1.674057 CTTCCTGCTGGAACGTCCT 59.326 57.895 20.15 0.00 46.57 3.85
4900 5737 0.390472 CTTCCTGCTGGAACGTCCTC 60.390 60.000 20.15 0.00 46.57 3.71
4901 5738 1.827399 TTCCTGCTGGAACGTCCTCC 61.827 60.000 20.15 0.00 46.57 4.30
4902 5739 2.286523 CCTGCTGGAACGTCCTCCT 61.287 63.158 2.92 0.00 37.46 3.69
4903 5740 0.970937 CCTGCTGGAACGTCCTCCTA 60.971 60.000 2.92 0.00 37.46 2.94
4904 5741 1.115467 CTGCTGGAACGTCCTCCTAT 58.885 55.000 7.76 0.00 37.46 2.57
4905 5742 1.482593 CTGCTGGAACGTCCTCCTATT 59.517 52.381 7.76 0.00 37.46 1.73
4906 5743 1.480954 TGCTGGAACGTCCTCCTATTC 59.519 52.381 7.76 0.00 37.46 1.75
4907 5744 1.202545 GCTGGAACGTCCTCCTATTCC 60.203 57.143 7.76 0.00 40.94 3.01
4908 5745 2.389715 CTGGAACGTCCTCCTATTCCT 58.610 52.381 7.76 0.00 41.11 3.36
4909 5746 2.766828 CTGGAACGTCCTCCTATTCCTT 59.233 50.000 7.76 0.00 41.11 3.36
4910 5747 3.178865 TGGAACGTCCTCCTATTCCTTT 58.821 45.455 7.76 0.00 41.11 3.11
4911 5748 3.197116 TGGAACGTCCTCCTATTCCTTTC 59.803 47.826 7.76 0.00 41.11 2.62
4912 5749 3.431905 GGAACGTCCTCCTATTCCTTTCC 60.432 52.174 0.00 0.00 38.08 3.13
4913 5750 3.117552 ACGTCCTCCTATTCCTTTCCT 57.882 47.619 0.00 0.00 0.00 3.36
4914 5751 3.451890 ACGTCCTCCTATTCCTTTCCTT 58.548 45.455 0.00 0.00 0.00 3.36
4915 5752 3.451540 ACGTCCTCCTATTCCTTTCCTTC 59.548 47.826 0.00 0.00 0.00 3.46
4916 5753 3.181464 CGTCCTCCTATTCCTTTCCTTCC 60.181 52.174 0.00 0.00 0.00 3.46
4917 5754 3.780850 GTCCTCCTATTCCTTTCCTTCCA 59.219 47.826 0.00 0.00 0.00 3.53
4918 5755 3.780850 TCCTCCTATTCCTTTCCTTCCAC 59.219 47.826 0.00 0.00 0.00 4.02
4919 5756 3.523564 CCTCCTATTCCTTTCCTTCCACA 59.476 47.826 0.00 0.00 0.00 4.17
4920 5757 4.018415 CCTCCTATTCCTTTCCTTCCACAA 60.018 45.833 0.00 0.00 0.00 3.33
4921 5758 5.340360 CCTCCTATTCCTTTCCTTCCACAAT 60.340 44.000 0.00 0.00 0.00 2.71
4922 5759 6.152638 TCCTATTCCTTTCCTTCCACAATT 57.847 37.500 0.00 0.00 0.00 2.32
4923 5760 6.187682 TCCTATTCCTTTCCTTCCACAATTC 58.812 40.000 0.00 0.00 0.00 2.17
4924 5761 5.360999 CCTATTCCTTTCCTTCCACAATTCC 59.639 44.000 0.00 0.00 0.00 3.01
4925 5762 3.169512 TCCTTTCCTTCCACAATTCCC 57.830 47.619 0.00 0.00 0.00 3.97
4926 5763 2.448961 TCCTTTCCTTCCACAATTCCCA 59.551 45.455 0.00 0.00 0.00 4.37
4927 5764 2.827921 CCTTTCCTTCCACAATTCCCAG 59.172 50.000 0.00 0.00 0.00 4.45
4928 5765 2.603075 TTCCTTCCACAATTCCCAGG 57.397 50.000 0.00 0.00 0.00 4.45
4929 5766 0.704076 TCCTTCCACAATTCCCAGGG 59.296 55.000 0.00 0.00 0.00 4.45
4930 5767 0.324645 CCTTCCACAATTCCCAGGGG 60.325 60.000 5.33 0.92 0.00 4.79
4931 5768 0.704076 CTTCCACAATTCCCAGGGGA 59.296 55.000 5.33 2.02 43.52 4.81
4932 5769 0.407918 TTCCACAATTCCCAGGGGAC 59.592 55.000 6.55 0.00 45.11 4.46
4933 5770 0.774096 TCCACAATTCCCAGGGGACA 60.774 55.000 6.55 0.00 45.11 4.02
4934 5771 0.114168 CCACAATTCCCAGGGGACAA 59.886 55.000 6.55 0.00 45.11 3.18
4935 5772 1.549203 CACAATTCCCAGGGGACAAG 58.451 55.000 6.55 2.15 45.11 3.16
4936 5773 0.409484 ACAATTCCCAGGGGACAAGG 59.591 55.000 6.55 0.00 45.11 3.61
4937 5774 0.409484 CAATTCCCAGGGGACAAGGT 59.591 55.000 6.55 0.00 45.11 3.50
4938 5775 0.409484 AATTCCCAGGGGACAAGGTG 59.591 55.000 6.55 0.00 45.11 4.00
4939 5776 0.776080 ATTCCCAGGGGACAAGGTGT 60.776 55.000 6.55 0.00 45.11 4.16
4940 5777 0.104356 TTCCCAGGGGACAAGGTGTA 60.104 55.000 6.55 0.00 45.11 2.90
4941 5778 0.546747 TCCCAGGGGACAAGGTGTAG 60.547 60.000 5.33 0.00 39.76 2.74
4942 5779 1.299976 CCAGGGGACAAGGTGTAGC 59.700 63.158 0.00 0.00 0.00 3.58
4943 5780 1.488705 CCAGGGGACAAGGTGTAGCA 61.489 60.000 0.00 0.00 0.00 3.49
4944 5781 0.400213 CAGGGGACAAGGTGTAGCAA 59.600 55.000 0.00 0.00 0.00 3.91
4945 5782 0.693049 AGGGGACAAGGTGTAGCAAG 59.307 55.000 0.00 0.00 0.00 4.01
4946 5783 0.322546 GGGGACAAGGTGTAGCAAGG 60.323 60.000 0.00 0.00 0.00 3.61
4947 5784 0.690762 GGGACAAGGTGTAGCAAGGA 59.309 55.000 0.00 0.00 0.00 3.36
4948 5785 1.610886 GGGACAAGGTGTAGCAAGGAC 60.611 57.143 0.00 0.00 0.00 3.85
4949 5786 1.071699 GGACAAGGTGTAGCAAGGACA 59.928 52.381 0.00 0.00 0.00 4.02
4950 5787 2.417719 GACAAGGTGTAGCAAGGACAG 58.582 52.381 0.00 0.00 0.00 3.51
4951 5788 1.768870 ACAAGGTGTAGCAAGGACAGT 59.231 47.619 0.00 0.00 0.00 3.55
4952 5789 2.146342 CAAGGTGTAGCAAGGACAGTG 58.854 52.381 0.00 0.00 0.00 3.66
4953 5790 1.424638 AGGTGTAGCAAGGACAGTGT 58.575 50.000 0.00 0.00 0.00 3.55
4954 5791 1.768870 AGGTGTAGCAAGGACAGTGTT 59.231 47.619 0.00 0.00 0.00 3.32
4955 5792 2.143925 GGTGTAGCAAGGACAGTGTTC 58.856 52.381 0.00 0.00 0.00 3.18
4956 5793 2.143925 GTGTAGCAAGGACAGTGTTCC 58.856 52.381 0.00 0.09 35.66 3.62
4965 5802 4.779993 AGGACAGTGTTCCTTTCTTCTT 57.220 40.909 0.00 0.00 44.22 2.52
4966 5803 4.709250 AGGACAGTGTTCCTTTCTTCTTC 58.291 43.478 0.00 0.00 44.22 2.87
4967 5804 4.410555 AGGACAGTGTTCCTTTCTTCTTCT 59.589 41.667 0.00 0.00 44.22 2.85
4968 5805 4.752604 GGACAGTGTTCCTTTCTTCTTCTC 59.247 45.833 0.00 0.00 32.24 2.87
4969 5806 4.709250 ACAGTGTTCCTTTCTTCTTCTCC 58.291 43.478 0.00 0.00 0.00 3.71
4970 5807 3.743396 CAGTGTTCCTTTCTTCTTCTCCG 59.257 47.826 0.00 0.00 0.00 4.63
4971 5808 3.388350 AGTGTTCCTTTCTTCTTCTCCGT 59.612 43.478 0.00 0.00 0.00 4.69
4972 5809 4.127907 GTGTTCCTTTCTTCTTCTCCGTT 58.872 43.478 0.00 0.00 0.00 4.44
4973 5810 4.024809 GTGTTCCTTTCTTCTTCTCCGTTG 60.025 45.833 0.00 0.00 0.00 4.10
4974 5811 3.402628 TCCTTTCTTCTTCTCCGTTGG 57.597 47.619 0.00 0.00 0.00 3.77
4975 5812 2.038557 TCCTTTCTTCTTCTCCGTTGGG 59.961 50.000 0.00 0.00 0.00 4.12
4976 5813 1.807142 CTTTCTTCTTCTCCGTTGGGC 59.193 52.381 0.00 0.00 0.00 5.36
4977 5814 0.762418 TTCTTCTTCTCCGTTGGGCA 59.238 50.000 0.00 0.00 0.00 5.36
4978 5815 0.984230 TCTTCTTCTCCGTTGGGCAT 59.016 50.000 0.00 0.00 0.00 4.40
4979 5816 1.089920 CTTCTTCTCCGTTGGGCATG 58.910 55.000 0.00 0.00 0.00 4.06
4980 5817 0.960364 TTCTTCTCCGTTGGGCATGC 60.960 55.000 9.90 9.90 0.00 4.06
4981 5818 1.377725 CTTCTCCGTTGGGCATGCT 60.378 57.895 18.92 0.00 0.00 3.79
4982 5819 1.651240 CTTCTCCGTTGGGCATGCTG 61.651 60.000 18.92 2.69 0.00 4.41
4983 5820 2.046023 CTCCGTTGGGCATGCTGA 60.046 61.111 18.92 0.79 0.00 4.26
4984 5821 1.452651 CTCCGTTGGGCATGCTGAT 60.453 57.895 18.92 0.00 0.00 2.90
4985 5822 1.001020 TCCGTTGGGCATGCTGATT 60.001 52.632 18.92 0.00 0.00 2.57
4986 5823 0.254462 TCCGTTGGGCATGCTGATTA 59.746 50.000 18.92 0.00 0.00 1.75
4987 5824 0.664761 CCGTTGGGCATGCTGATTAG 59.335 55.000 18.92 5.22 0.00 1.73
4988 5825 1.667236 CGTTGGGCATGCTGATTAGA 58.333 50.000 18.92 0.00 0.00 2.10
4989 5826 2.224606 CGTTGGGCATGCTGATTAGAT 58.775 47.619 18.92 0.00 0.00 1.98
4990 5827 2.031420 CGTTGGGCATGCTGATTAGATG 60.031 50.000 18.92 0.00 0.00 2.90
4991 5828 2.281539 TGGGCATGCTGATTAGATGG 57.718 50.000 18.92 0.00 0.00 3.51
4992 5829 1.202964 TGGGCATGCTGATTAGATGGG 60.203 52.381 18.92 0.00 0.00 4.00
4993 5830 0.886563 GGCATGCTGATTAGATGGGC 59.113 55.000 18.92 0.00 0.00 5.36
4994 5831 0.520404 GCATGCTGATTAGATGGGCG 59.480 55.000 11.37 0.00 0.00 6.13
4995 5832 1.879372 GCATGCTGATTAGATGGGCGA 60.879 52.381 11.37 0.00 0.00 5.54
4996 5833 2.708051 CATGCTGATTAGATGGGCGAT 58.292 47.619 0.00 0.00 0.00 4.58
4997 5834 2.462456 TGCTGATTAGATGGGCGATC 57.538 50.000 0.65 0.65 0.00 3.69
4998 5835 1.002430 TGCTGATTAGATGGGCGATCC 59.998 52.381 5.83 0.00 0.00 3.36
4999 5836 1.277557 GCTGATTAGATGGGCGATCCT 59.722 52.381 5.83 0.00 36.20 3.24
5000 5837 2.934364 GCTGATTAGATGGGCGATCCTG 60.934 54.545 5.83 0.00 36.20 3.86
5001 5838 1.002430 TGATTAGATGGGCGATCCTGC 59.998 52.381 5.83 0.00 36.20 4.85
5009 5846 2.044946 GCGATCCTGCCCCAAACT 60.045 61.111 0.00 0.00 0.00 2.66
5010 5847 1.678970 GCGATCCTGCCCCAAACTT 60.679 57.895 0.00 0.00 0.00 2.66
5011 5848 1.937546 GCGATCCTGCCCCAAACTTG 61.938 60.000 0.00 0.00 0.00 3.16
5012 5849 1.893062 GATCCTGCCCCAAACTTGC 59.107 57.895 0.00 0.00 0.00 4.01
5013 5850 0.613012 GATCCTGCCCCAAACTTGCT 60.613 55.000 0.00 0.00 0.00 3.91
5014 5851 0.178924 ATCCTGCCCCAAACTTGCTT 60.179 50.000 0.00 0.00 0.00 3.91
5015 5852 1.114722 TCCTGCCCCAAACTTGCTTG 61.115 55.000 0.00 0.00 0.00 4.01
5016 5853 1.368579 CTGCCCCAAACTTGCTTGG 59.631 57.895 0.00 0.00 44.77 3.61
5023 5860 2.443887 CAAACTTGCTTGGACCATGG 57.556 50.000 11.19 11.19 0.00 3.66
5024 5861 0.681175 AAACTTGCTTGGACCATGGC 59.319 50.000 13.04 10.55 0.00 4.40
5025 5862 1.187567 AACTTGCTTGGACCATGGCC 61.188 55.000 13.04 14.81 0.00 5.36
5026 5863 1.607178 CTTGCTTGGACCATGGCCA 60.607 57.895 20.10 20.10 0.00 5.36
5027 5864 1.152376 TTGCTTGGACCATGGCCAA 60.152 52.632 28.06 28.06 42.81 4.52
5028 5865 0.544833 TTGCTTGGACCATGGCCAAT 60.545 50.000 29.28 6.69 43.90 3.16
5029 5866 0.971959 TGCTTGGACCATGGCCAATC 60.972 55.000 29.28 26.35 43.90 2.67
5030 5867 1.679559 GCTTGGACCATGGCCAATCC 61.680 60.000 29.28 21.55 43.90 3.01
5038 5875 4.749323 TGGCCAATCCAGAGCAAG 57.251 55.556 0.61 0.00 40.72 4.01
5039 5876 1.769665 TGGCCAATCCAGAGCAAGT 59.230 52.632 0.61 0.00 40.72 3.16
5040 5877 0.609957 TGGCCAATCCAGAGCAAGTG 60.610 55.000 0.61 0.00 40.72 3.16
5041 5878 1.509923 GCCAATCCAGAGCAAGTGC 59.490 57.895 0.00 0.00 42.49 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.651225 GCAACTATCAAGGAAGTAAGAAGTGT 59.349 38.462 0.00 0.00 0.00 3.55
1 2 6.183360 CGCAACTATCAAGGAAGTAAGAAGTG 60.183 42.308 0.00 0.00 0.00 3.16
18 19 2.586258 ATCTCGCTTGACGCAACTAT 57.414 45.000 0.00 0.00 43.23 2.12
143 144 0.401395 AGGACTTGAACCCTGGTGGA 60.401 55.000 0.00 0.00 38.00 4.02
191 192 5.006649 CGAAAGCACATCATCGAAAATCCTA 59.993 40.000 0.00 0.00 37.48 2.94
202 203 2.086869 CTTCCACCGAAAGCACATCAT 58.913 47.619 0.00 0.00 0.00 2.45
203 204 1.071542 TCTTCCACCGAAAGCACATCA 59.928 47.619 0.00 0.00 0.00 3.07
215 216 2.735762 GCTCGTACACTCATCTTCCACC 60.736 54.545 0.00 0.00 0.00 4.61
220 221 0.811915 AGCGCTCGTACACTCATCTT 59.188 50.000 2.64 0.00 0.00 2.40
223 224 1.078759 GCAAGCGCTCGTACACTCAT 61.079 55.000 12.06 0.00 34.30 2.90
322 582 4.927267 ACATCTTCTACCATGGGTCAAA 57.073 40.909 18.09 3.90 37.09 2.69
394 654 4.570772 CCGAAGAGGGTGTATACAATGTTG 59.429 45.833 7.25 0.00 35.97 3.33
396 656 3.431766 GCCGAAGAGGGTGTATACAATGT 60.432 47.826 7.25 0.00 41.48 2.71
402 662 1.855295 TGTGCCGAAGAGGGTGTATA 58.145 50.000 0.00 0.00 41.48 1.47
403 663 0.981183 TTGTGCCGAAGAGGGTGTAT 59.019 50.000 0.00 0.00 41.48 2.29
623 883 6.017934 TGTGTCTCTACTGCAAAATCTTTGAC 60.018 38.462 3.35 0.00 0.00 3.18
652 912 9.938280 ATAGGCAACAATAAATAGCGACTAATA 57.062 29.630 0.00 0.00 41.41 0.98
656 916 5.470098 CCATAGGCAACAATAAATAGCGACT 59.530 40.000 0.00 0.00 41.41 4.18
756 1016 4.137543 GCGAGGATTTATGAGGAATTGGT 58.862 43.478 0.00 0.00 0.00 3.67
830 1090 4.760047 GCGGGGAAGCAGCGAGAA 62.760 66.667 0.00 0.00 37.05 2.87
897 1169 3.660501 CACTAGGTGCTTGGCGATATA 57.339 47.619 0.00 0.00 0.00 0.86
1115 1417 2.358369 TCTCCTCGACGTCACGCT 60.358 61.111 17.16 0.00 0.00 5.07
1260 1562 1.586422 GCATCGGCATGTACACATCT 58.414 50.000 0.00 0.00 40.72 2.90
1265 1567 0.463654 GAAGGGCATCGGCATGTACA 60.464 55.000 0.00 0.00 43.71 2.90
1334 1636 5.946298 TGCAAACTGAGATGACAATCAATC 58.054 37.500 0.00 0.00 35.03 2.67
1413 1742 9.381038 AGACAATTGTATGACAGGGTATATACT 57.619 33.333 11.95 0.00 0.00 2.12
1444 1773 4.035091 GGTCGCATGCACAATATGAACTAA 59.965 41.667 19.57 0.00 0.00 2.24
1603 1932 1.271379 ACATACCTCGCTTGTGCCTTT 60.271 47.619 0.00 0.00 35.36 3.11
1661 1990 9.566432 AAAGAGAAGAAAAACTCACATACAGAT 57.434 29.630 0.00 0.00 35.83 2.90
1901 2230 2.885894 TCACTCAAACTGAATGCATGCA 59.114 40.909 25.04 25.04 0.00 3.96
1924 2253 0.597568 CAAGCTTTCACATCGGGCAA 59.402 50.000 0.00 0.00 0.00 4.52
1944 2273 6.128336 GCAGATGAATGATACTAACATCAGCC 60.128 42.308 0.00 0.00 41.27 4.85
1997 2326 5.112220 TGAACGTGTTGTTATCGTCTAGT 57.888 39.130 0.00 0.00 42.09 2.57
2119 2448 5.984926 GTCATTTCAATGTTTCCTGAAAGCA 59.015 36.000 3.89 0.00 42.96 3.91
2166 2495 4.847757 CGTAGTTGCATCACAAATTCACAG 59.152 41.667 0.00 0.00 40.82 3.66
2174 2503 3.106242 AGTGTCGTAGTTGCATCACAA 57.894 42.857 0.00 0.00 35.33 3.33
2231 2560 9.910511 CTTAAGAAAAATATTGATGCAATGTGC 57.089 29.630 0.00 0.00 45.29 4.57
2315 2644 6.684613 GCAACATCTTGCCCAATCTGATTATT 60.685 38.462 1.98 0.00 46.27 1.40
2801 3133 2.799126 AATGGTATTTGCGGAGGACA 57.201 45.000 0.00 0.00 0.00 4.02
2833 3165 7.559335 AGGTGTCTCATTATGGAAGCATATA 57.441 36.000 0.00 0.00 0.00 0.86
2857 3189 7.886629 ACGAGTTACCTGGTCATAGTAATTA 57.113 36.000 0.63 0.00 0.00 1.40
2925 3258 6.603201 ACCCTAATGTGGTTAAATGTCATCAG 59.397 38.462 0.00 0.00 29.75 2.90
2972 3305 4.166725 TCTTGCAATCTCCCCAAGATACAT 59.833 41.667 0.00 0.00 44.26 2.29
3170 3992 6.212888 AGCAAATCCAATGTCTACAAATCC 57.787 37.500 0.00 0.00 0.00 3.01
3269 4093 7.518188 AGGTGTATGGCAAGCTAAATATAAGT 58.482 34.615 0.00 0.00 0.00 2.24
3270 4094 7.148573 CGAGGTGTATGGCAAGCTAAATATAAG 60.149 40.741 0.00 0.00 0.00 1.73
3271 4095 6.649141 CGAGGTGTATGGCAAGCTAAATATAA 59.351 38.462 0.00 0.00 0.00 0.98
3287 4111 2.072487 AGGCCCATGCGAGGTGTAT 61.072 57.895 0.00 0.00 38.85 2.29
3338 4172 7.016361 ACATCTGAAGTGTACAAAACTTGAC 57.984 36.000 0.00 0.00 37.98 3.18
3404 4239 6.529125 GGAAGTGCAAGATGTTCATTGTTATG 59.471 38.462 0.00 0.00 0.00 1.90
3523 4358 5.246883 TCAAGTCAAGAGAATCATCCTCACA 59.753 40.000 0.00 0.00 37.82 3.58
3732 4567 2.047655 CGTGCGGCTCTTTGGGTA 60.048 61.111 0.00 0.00 0.00 3.69
3780 4615 2.034053 TCCATCACGACCAAGTTTTTGC 59.966 45.455 0.00 0.00 32.79 3.68
3807 4642 1.587054 GACTCTCGTGGTCCCACAG 59.413 63.158 16.27 11.95 46.47 3.66
3813 4648 1.446907 TACTTCGGACTCTCGTGGTC 58.553 55.000 0.00 0.00 0.00 4.02
3909 4744 0.523072 CCAACACGGCTTCATTCAGG 59.477 55.000 0.00 0.00 0.00 3.86
3991 4826 3.001514 GATGAGAGCAGCCCCCAA 58.998 61.111 0.00 0.00 0.00 4.12
4091 4926 2.684881 CCTGCAGTATGAATGAACACCC 59.315 50.000 13.81 0.00 39.69 4.61
4092 4927 2.684881 CCCTGCAGTATGAATGAACACC 59.315 50.000 13.81 0.00 39.69 4.16
4118 4953 8.413229 CCCACATAAAAATACACCCATTCTAAG 58.587 37.037 0.00 0.00 0.00 2.18
4171 5006 2.897271 TGTGTGGGCATTGGTATTCT 57.103 45.000 0.00 0.00 0.00 2.40
4263 5098 3.587797 TCAGACACCGACTTAACATCC 57.412 47.619 0.00 0.00 0.00 3.51
4275 5110 5.635280 CGGATTCACATATACATCAGACACC 59.365 44.000 0.00 0.00 0.00 4.16
4404 5240 5.592282 TGCAACATAGAGAAAGTGGAAAACA 59.408 36.000 0.00 0.00 0.00 2.83
4451 5287 1.209019 CCAGCCAGTGAACTGCTAGAT 59.791 52.381 4.87 0.00 42.47 1.98
4546 5382 2.421424 CGGCAAGAATTTCTTCCTCCTG 59.579 50.000 8.71 0.00 33.78 3.86
4593 5429 0.320771 ATGTTGGACGCACTCCTGTC 60.321 55.000 0.00 0.00 40.26 3.51
4596 5432 0.108585 AACATGTTGGACGCACTCCT 59.891 50.000 11.07 0.00 40.26 3.69
4638 5474 1.206578 CGGAACAACATGCACCGTC 59.793 57.895 1.75 0.00 35.67 4.79
4730 5566 2.069273 GCTTGTTCTCTTAGCTTGCGA 58.931 47.619 0.00 0.00 32.26 5.10
4837 5674 3.251245 TCACGCGATTAAGAGAGGAGATC 59.749 47.826 15.93 0.00 0.00 2.75
4838 5675 3.003897 GTCACGCGATTAAGAGAGGAGAT 59.996 47.826 15.93 0.00 0.00 2.75
4839 5676 2.355132 GTCACGCGATTAAGAGAGGAGA 59.645 50.000 15.93 0.00 0.00 3.71
4840 5677 2.722071 GTCACGCGATTAAGAGAGGAG 58.278 52.381 15.93 0.00 0.00 3.69
4841 5678 1.063616 CGTCACGCGATTAAGAGAGGA 59.936 52.381 15.93 0.00 44.77 3.71
4842 5679 1.063616 TCGTCACGCGATTAAGAGAGG 59.936 52.381 15.93 4.72 45.68 3.69
4843 5680 2.453650 TCGTCACGCGATTAAGAGAG 57.546 50.000 15.93 0.33 45.68 3.20
4853 5690 2.213575 GCTTAGACTATTTCGTCACGCG 59.786 50.000 3.53 3.53 43.01 6.01
4854 5691 3.436496 AGCTTAGACTATTTCGTCACGC 58.564 45.455 0.00 0.00 36.38 5.34
4855 5692 4.659088 TGAGCTTAGACTATTTCGTCACG 58.341 43.478 0.00 0.00 36.38 4.35
4856 5693 6.361214 GCTATGAGCTTAGACTATTTCGTCAC 59.639 42.308 0.00 0.00 38.45 3.67
4857 5694 6.439599 GCTATGAGCTTAGACTATTTCGTCA 58.560 40.000 0.00 0.00 38.45 4.35
4858 5695 6.921332 GCTATGAGCTTAGACTATTTCGTC 57.079 41.667 0.00 0.00 38.45 4.20
4883 5720 2.283529 GGAGGACGTTCCAGCAGGA 61.284 63.158 1.23 0.00 43.93 3.86
4884 5721 0.970937 TAGGAGGACGTTCCAGCAGG 60.971 60.000 8.93 0.00 39.61 4.85
4885 5722 1.115467 ATAGGAGGACGTTCCAGCAG 58.885 55.000 8.93 0.00 39.61 4.24
4886 5723 1.480954 GAATAGGAGGACGTTCCAGCA 59.519 52.381 8.93 0.00 39.61 4.41
4887 5724 1.202545 GGAATAGGAGGACGTTCCAGC 60.203 57.143 8.93 0.02 39.61 4.85
4888 5725 2.389715 AGGAATAGGAGGACGTTCCAG 58.610 52.381 8.93 0.00 39.61 3.86
4889 5726 2.544844 AGGAATAGGAGGACGTTCCA 57.455 50.000 8.93 0.00 39.61 3.53
4890 5727 3.431905 GGAAAGGAATAGGAGGACGTTCC 60.432 52.174 0.00 0.00 38.34 3.62
4891 5728 3.451540 AGGAAAGGAATAGGAGGACGTTC 59.548 47.826 0.00 0.00 0.00 3.95
4892 5729 3.451890 AGGAAAGGAATAGGAGGACGTT 58.548 45.455 0.00 0.00 0.00 3.99
4893 5730 3.117552 AGGAAAGGAATAGGAGGACGT 57.882 47.619 0.00 0.00 0.00 4.34
4894 5731 3.181464 GGAAGGAAAGGAATAGGAGGACG 60.181 52.174 0.00 0.00 0.00 4.79
4895 5732 3.780850 TGGAAGGAAAGGAATAGGAGGAC 59.219 47.826 0.00 0.00 0.00 3.85
4896 5733 3.780850 GTGGAAGGAAAGGAATAGGAGGA 59.219 47.826 0.00 0.00 0.00 3.71
4897 5734 3.523564 TGTGGAAGGAAAGGAATAGGAGG 59.476 47.826 0.00 0.00 0.00 4.30
4898 5735 4.844349 TGTGGAAGGAAAGGAATAGGAG 57.156 45.455 0.00 0.00 0.00 3.69
4899 5736 5.796502 ATTGTGGAAGGAAAGGAATAGGA 57.203 39.130 0.00 0.00 0.00 2.94
4900 5737 5.360999 GGAATTGTGGAAGGAAAGGAATAGG 59.639 44.000 0.00 0.00 0.00 2.57
4901 5738 5.360999 GGGAATTGTGGAAGGAAAGGAATAG 59.639 44.000 0.00 0.00 0.00 1.73
4902 5739 5.222442 TGGGAATTGTGGAAGGAAAGGAATA 60.222 40.000 0.00 0.00 0.00 1.75
4903 5740 4.096681 GGGAATTGTGGAAGGAAAGGAAT 58.903 43.478 0.00 0.00 0.00 3.01
4904 5741 3.116939 TGGGAATTGTGGAAGGAAAGGAA 60.117 43.478 0.00 0.00 0.00 3.36
4905 5742 2.448961 TGGGAATTGTGGAAGGAAAGGA 59.551 45.455 0.00 0.00 0.00 3.36
4906 5743 2.827921 CTGGGAATTGTGGAAGGAAAGG 59.172 50.000 0.00 0.00 0.00 3.11
4907 5744 2.827921 CCTGGGAATTGTGGAAGGAAAG 59.172 50.000 0.00 0.00 0.00 2.62
4908 5745 2.492567 CCCTGGGAATTGTGGAAGGAAA 60.493 50.000 7.01 0.00 0.00 3.13
4909 5746 1.077005 CCCTGGGAATTGTGGAAGGAA 59.923 52.381 7.01 0.00 0.00 3.36
4910 5747 0.704076 CCCTGGGAATTGTGGAAGGA 59.296 55.000 7.01 0.00 0.00 3.36
4911 5748 0.324645 CCCCTGGGAATTGTGGAAGG 60.325 60.000 16.20 0.00 37.50 3.46
4912 5749 0.704076 TCCCCTGGGAATTGTGGAAG 59.296 55.000 16.20 0.00 42.05 3.46
4913 5750 2.890258 TCCCCTGGGAATTGTGGAA 58.110 52.632 16.20 0.00 42.05 3.53
4914 5751 4.700887 TCCCCTGGGAATTGTGGA 57.299 55.556 16.20 0.00 42.05 4.02
4922 5759 0.546747 CTACACCTTGTCCCCTGGGA 60.547 60.000 16.20 3.95 42.90 4.37
4923 5760 1.991230 CTACACCTTGTCCCCTGGG 59.009 63.158 5.50 5.50 0.00 4.45
4924 5761 1.299976 GCTACACCTTGTCCCCTGG 59.700 63.158 0.00 0.00 0.00 4.45
4925 5762 0.400213 TTGCTACACCTTGTCCCCTG 59.600 55.000 0.00 0.00 0.00 4.45
4926 5763 0.693049 CTTGCTACACCTTGTCCCCT 59.307 55.000 0.00 0.00 0.00 4.79
4927 5764 0.322546 CCTTGCTACACCTTGTCCCC 60.323 60.000 0.00 0.00 0.00 4.81
4928 5765 0.690762 TCCTTGCTACACCTTGTCCC 59.309 55.000 0.00 0.00 0.00 4.46
4929 5766 1.071699 TGTCCTTGCTACACCTTGTCC 59.928 52.381 0.00 0.00 0.00 4.02
4930 5767 2.224305 ACTGTCCTTGCTACACCTTGTC 60.224 50.000 0.00 0.00 0.00 3.18
4931 5768 1.768870 ACTGTCCTTGCTACACCTTGT 59.231 47.619 0.00 0.00 0.00 3.16
4932 5769 2.146342 CACTGTCCTTGCTACACCTTG 58.854 52.381 0.00 0.00 0.00 3.61
4933 5770 1.768870 ACACTGTCCTTGCTACACCTT 59.231 47.619 0.00 0.00 0.00 3.50
4934 5771 1.424638 ACACTGTCCTTGCTACACCT 58.575 50.000 0.00 0.00 0.00 4.00
4935 5772 2.143925 GAACACTGTCCTTGCTACACC 58.856 52.381 0.00 0.00 0.00 4.16
4936 5773 2.143925 GGAACACTGTCCTTGCTACAC 58.856 52.381 0.00 0.00 34.56 2.90
4937 5774 2.047061 AGGAACACTGTCCTTGCTACA 58.953 47.619 0.00 0.00 46.42 2.74
4938 5775 2.841442 AGGAACACTGTCCTTGCTAC 57.159 50.000 0.00 0.00 46.42 3.58
4945 5782 4.709250 AGAAGAAGAAAGGAACACTGTCC 58.291 43.478 0.00 0.00 33.59 4.02
4946 5783 4.752604 GGAGAAGAAGAAAGGAACACTGTC 59.247 45.833 0.00 0.00 33.27 3.51
4947 5784 4.709250 GGAGAAGAAGAAAGGAACACTGT 58.291 43.478 0.00 0.00 0.00 3.55
4948 5785 3.743396 CGGAGAAGAAGAAAGGAACACTG 59.257 47.826 0.00 0.00 0.00 3.66
4949 5786 3.388350 ACGGAGAAGAAGAAAGGAACACT 59.612 43.478 0.00 0.00 0.00 3.55
4950 5787 3.729966 ACGGAGAAGAAGAAAGGAACAC 58.270 45.455 0.00 0.00 0.00 3.32
4951 5788 4.127171 CAACGGAGAAGAAGAAAGGAACA 58.873 43.478 0.00 0.00 0.00 3.18
4952 5789 3.498777 CCAACGGAGAAGAAGAAAGGAAC 59.501 47.826 0.00 0.00 0.00 3.62
4953 5790 3.496160 CCCAACGGAGAAGAAGAAAGGAA 60.496 47.826 0.00 0.00 0.00 3.36
4954 5791 2.038557 CCCAACGGAGAAGAAGAAAGGA 59.961 50.000 0.00 0.00 0.00 3.36
4955 5792 2.427506 CCCAACGGAGAAGAAGAAAGG 58.572 52.381 0.00 0.00 0.00 3.11
4956 5793 1.807142 GCCCAACGGAGAAGAAGAAAG 59.193 52.381 0.00 0.00 0.00 2.62
4957 5794 1.142060 TGCCCAACGGAGAAGAAGAAA 59.858 47.619 0.00 0.00 0.00 2.52
4958 5795 0.762418 TGCCCAACGGAGAAGAAGAA 59.238 50.000 0.00 0.00 0.00 2.52
4959 5796 0.984230 ATGCCCAACGGAGAAGAAGA 59.016 50.000 0.00 0.00 0.00 2.87
4960 5797 1.089920 CATGCCCAACGGAGAAGAAG 58.910 55.000 0.00 0.00 0.00 2.85
4961 5798 0.960364 GCATGCCCAACGGAGAAGAA 60.960 55.000 6.36 0.00 0.00 2.52
4962 5799 1.377202 GCATGCCCAACGGAGAAGA 60.377 57.895 6.36 0.00 0.00 2.87
4963 5800 1.377725 AGCATGCCCAACGGAGAAG 60.378 57.895 15.66 0.00 0.00 2.85
4964 5801 1.675310 CAGCATGCCCAACGGAGAA 60.675 57.895 15.66 0.00 0.00 2.87
4965 5802 1.913951 ATCAGCATGCCCAACGGAGA 61.914 55.000 15.66 0.24 34.76 3.71
4966 5803 1.033746 AATCAGCATGCCCAACGGAG 61.034 55.000 15.66 0.00 34.76 4.63
4967 5804 0.254462 TAATCAGCATGCCCAACGGA 59.746 50.000 15.66 3.16 34.76 4.69
4968 5805 0.664761 CTAATCAGCATGCCCAACGG 59.335 55.000 15.66 0.00 34.76 4.44
4969 5806 1.667236 TCTAATCAGCATGCCCAACG 58.333 50.000 15.66 0.00 34.76 4.10
4970 5807 2.295349 CCATCTAATCAGCATGCCCAAC 59.705 50.000 15.66 0.00 34.76 3.77
4971 5808 2.589720 CCATCTAATCAGCATGCCCAA 58.410 47.619 15.66 0.00 34.76 4.12
4972 5809 1.202964 CCCATCTAATCAGCATGCCCA 60.203 52.381 15.66 0.33 34.76 5.36
4973 5810 1.542492 CCCATCTAATCAGCATGCCC 58.458 55.000 15.66 0.00 34.76 5.36
4974 5811 0.886563 GCCCATCTAATCAGCATGCC 59.113 55.000 15.66 0.00 34.76 4.40
4975 5812 0.520404 CGCCCATCTAATCAGCATGC 59.480 55.000 10.51 10.51 34.76 4.06
4976 5813 2.174363 TCGCCCATCTAATCAGCATG 57.826 50.000 0.00 0.00 37.54 4.06
4977 5814 2.355513 GGATCGCCCATCTAATCAGCAT 60.356 50.000 0.00 0.00 34.14 3.79
4978 5815 1.002430 GGATCGCCCATCTAATCAGCA 59.998 52.381 0.00 0.00 34.14 4.41
4979 5816 1.277557 AGGATCGCCCATCTAATCAGC 59.722 52.381 0.00 0.00 37.41 4.26
4980 5817 2.934364 GCAGGATCGCCCATCTAATCAG 60.934 54.545 0.00 0.00 37.41 2.90
4981 5818 1.002430 GCAGGATCGCCCATCTAATCA 59.998 52.381 0.00 0.00 37.41 2.57
4982 5819 1.731720 GCAGGATCGCCCATCTAATC 58.268 55.000 0.00 0.00 37.41 1.75
4983 5820 3.944476 GCAGGATCGCCCATCTAAT 57.056 52.632 0.00 0.00 37.41 1.73
4992 5829 1.678970 AAGTTTGGGGCAGGATCGC 60.679 57.895 0.00 0.00 0.00 4.58
4993 5830 1.937546 GCAAGTTTGGGGCAGGATCG 61.938 60.000 0.00 0.00 0.00 3.69
4994 5831 0.613012 AGCAAGTTTGGGGCAGGATC 60.613 55.000 0.00 0.00 0.00 3.36
4995 5832 0.178924 AAGCAAGTTTGGGGCAGGAT 60.179 50.000 0.00 0.00 0.00 3.24
4996 5833 1.114722 CAAGCAAGTTTGGGGCAGGA 61.115 55.000 0.00 0.00 0.00 3.86
4997 5834 1.368579 CAAGCAAGTTTGGGGCAGG 59.631 57.895 0.00 0.00 0.00 4.85
4998 5835 1.114722 TCCAAGCAAGTTTGGGGCAG 61.115 55.000 14.47 0.00 46.16 4.85
4999 5836 1.075674 TCCAAGCAAGTTTGGGGCA 60.076 52.632 14.47 0.00 46.16 5.36
5000 5837 1.367471 GTCCAAGCAAGTTTGGGGC 59.633 57.895 14.47 5.84 46.16 5.80
5001 5838 0.758685 TGGTCCAAGCAAGTTTGGGG 60.759 55.000 14.47 0.00 46.16 4.96
5002 5839 1.001181 CATGGTCCAAGCAAGTTTGGG 59.999 52.381 14.47 0.00 46.16 4.12
5004 5841 1.606224 GCCATGGTCCAAGCAAGTTTG 60.606 52.381 14.67 0.00 0.00 2.93
5005 5842 0.681175 GCCATGGTCCAAGCAAGTTT 59.319 50.000 14.67 0.00 0.00 2.66
5006 5843 1.187567 GGCCATGGTCCAAGCAAGTT 61.188 55.000 14.67 0.00 0.00 2.66
5007 5844 1.607467 GGCCATGGTCCAAGCAAGT 60.607 57.895 14.67 0.00 0.00 3.16
5008 5845 1.186917 TTGGCCATGGTCCAAGCAAG 61.187 55.000 27.00 0.00 38.57 4.01
5009 5846 0.544833 ATTGGCCATGGTCCAAGCAA 60.545 50.000 31.06 17.88 45.69 3.91
5010 5847 0.971959 GATTGGCCATGGTCCAAGCA 60.972 55.000 32.91 19.44 46.18 3.91
5011 5848 1.679559 GGATTGGCCATGGTCCAAGC 61.680 60.000 31.44 31.44 45.69 4.01
5012 5849 0.324552 TGGATTGGCCATGGTCCAAG 60.325 55.000 31.06 3.86 45.69 3.61
5013 5850 1.779653 TGGATTGGCCATGGTCCAA 59.220 52.632 30.42 30.42 46.44 3.53
5014 5851 3.518035 TGGATTGGCCATGGTCCA 58.482 55.556 23.76 23.76 43.33 4.02
5021 5858 0.609957 CACTTGCTCTGGATTGGCCA 60.610 55.000 0.00 0.00 46.96 5.36
5022 5859 1.941999 GCACTTGCTCTGGATTGGCC 61.942 60.000 0.00 0.00 38.21 5.36
5023 5860 1.509923 GCACTTGCTCTGGATTGGC 59.490 57.895 0.00 0.00 38.21 4.52
5024 5861 0.957395 ACGCACTTGCTCTGGATTGG 60.957 55.000 0.00 0.00 39.32 3.16
5025 5862 0.445436 GACGCACTTGCTCTGGATTG 59.555 55.000 0.00 0.00 39.32 2.67
5026 5863 1.016130 CGACGCACTTGCTCTGGATT 61.016 55.000 0.00 0.00 39.32 3.01
5027 5864 1.446792 CGACGCACTTGCTCTGGAT 60.447 57.895 0.00 0.00 39.32 3.41
5028 5865 1.520600 TACGACGCACTTGCTCTGGA 61.521 55.000 0.00 0.00 39.32 3.86
5029 5866 1.080772 TACGACGCACTTGCTCTGG 60.081 57.895 0.00 0.00 39.32 3.86
5030 5867 4.552278 TACGACGCACTTGCTCTG 57.448 55.556 0.00 0.00 39.32 3.35


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

AutoCloner maintained by Alex Coulton.