Multiple sequence alignment - TraesCS1B01G228000

Loading Multiple Alignment...

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 TraesCS1B01G228000 chr1B 100.000 3923 0 0 1 3923 409624064 409620142 0.000000e+00 7245.0
1 TraesCS1B01G228000 chr1B 100.000 3401 0 0 4080 7480 409619985 409616585 0.000000e+00 6281.0
2 TraesCS1B01G228000 chr1B 90.470 724 62 6 6737 7459 162187038 162187755 0.000000e+00 948.0
3 TraesCS1B01G228000 chr1B 87.654 243 23 3 4859 5101 163659064 163658829 7.390000e-70 276.0
4 TraesCS1B01G228000 chr1B 86.831 243 25 2 4859 5101 133707301 133707536 1.600000e-66 265.0
5 TraesCS1B01G228000 chr1B 87.565 193 20 4 5150 5339 133707544 133707735 3.510000e-53 220.0
6 TraesCS1B01G228000 chr1B 86.528 193 22 4 5150 5339 163658821 163658630 7.610000e-50 209.0
7 TraesCS1B01G228000 chr1B 91.071 112 9 1 5150 5260 102623051 102622940 4.680000e-32 150.0
8 TraesCS1B01G228000 chr1B 83.448 145 23 1 51 195 623968940 623969083 4.710000e-27 134.0
9 TraesCS1B01G228000 chr1D 94.284 3184 119 35 765 3923 302710876 302707731 0.000000e+00 4813.0
10 TraesCS1B01G228000 chr1D 95.019 2590 95 19 4163 6734 302707384 302704811 0.000000e+00 4037.0
11 TraesCS1B01G228000 chr1D 89.474 114 9 3 2241 2352 302709932 302709820 2.810000e-29 141.0
12 TraesCS1B01G228000 chr1D 94.828 58 2 1 4112 4168 302707469 302707412 1.030000e-13 89.8
13 TraesCS1B01G228000 chr1A 95.494 2663 75 16 4084 6733 377225450 377222820 0.000000e+00 4211.0
14 TraesCS1B01G228000 chr1A 95.189 2245 86 13 1686 3923 377227855 377225626 0.000000e+00 3528.0
15 TraesCS1B01G228000 chr1A 91.732 1669 102 17 8 1663 377229556 377227911 0.000000e+00 2285.0
16 TraesCS1B01G228000 chr7B 89.302 673 64 7 6801 7470 438373515 438374182 0.000000e+00 837.0
17 TraesCS1B01G228000 chr7B 90.566 106 8 2 5151 5254 677702950 677702845 1.010000e-28 139.0
18 TraesCS1B01G228000 chr4B 85.906 745 96 9 6738 7479 214742950 214742212 0.000000e+00 785.0
19 TraesCS1B01G228000 chr4B 83.871 124 15 4 78 198 664202761 664202882 6.130000e-21 113.0
20 TraesCS1B01G228000 chr6A 84.906 742 101 11 6740 7476 147954609 147953874 0.000000e+00 739.0
21 TraesCS1B01G228000 chr6A 84.553 738 96 17 6740 7470 102993850 102993124 0.000000e+00 715.0
22 TraesCS1B01G228000 chr5A 84.812 744 96 15 6739 7476 383828226 383827494 0.000000e+00 732.0
23 TraesCS1B01G228000 chr5A 84.168 739 104 12 6735 7468 314741651 314740921 0.000000e+00 704.0
24 TraesCS1B01G228000 chr7A 84.011 738 106 12 6740 7472 139443986 139443256 0.000000e+00 699.0
25 TraesCS1B01G228000 chr7A 83.780 746 103 14 6740 7476 701400132 701399396 0.000000e+00 691.0
26 TraesCS1B01G228000 chr7A 86.275 255 24 6 4859 5113 690945148 690944905 4.450000e-67 267.0
27 TraesCS1B01G228000 chr3D 88.066 243 22 2 4859 5101 583137341 583137106 1.590000e-71 281.0
28 TraesCS1B01G228000 chr3D 86.161 224 21 3 4859 5082 552658111 552657898 4.510000e-57 233.0
29 TraesCS1B01G228000 chr3D 88.144 194 21 2 5150 5342 552655854 552655662 5.840000e-56 230.0
30 TraesCS1B01G228000 chr3D 85.268 224 23 3 4859 5082 552653938 552653725 9.770000e-54 222.0
31 TraesCS1B01G228000 chr3D 86.667 195 18 4 5150 5339 583137098 583136907 7.610000e-50 209.0
32 TraesCS1B01G228000 chr3D 79.134 254 39 12 243 488 177367622 177367869 6.010000e-36 163.0
33 TraesCS1B01G228000 chr3D 100.000 30 0 0 404 433 170811199 170811228 1.000000e-03 56.5
34 TraesCS1B01G228000 chr2D 87.059 255 26 2 4859 5113 512841431 512841678 1.590000e-71 281.0
35 TraesCS1B01G228000 chr2D 90.226 133 9 2 5151 5282 512841683 512841812 3.590000e-38 171.0
36 TraesCS1B01G228000 chr2D 81.046 153 20 5 51 194 511936433 511936585 6.130000e-21 113.0
37 TraesCS1B01G228000 chr2B 85.098 255 30 3 4859 5113 603194565 603194811 3.460000e-63 254.0
38 TraesCS1B01G228000 chr6D 84.706 255 28 3 4859 5113 84287026 84286783 2.080000e-60 244.0
39 TraesCS1B01G228000 chr5B 83.012 259 31 7 4859 5113 92198127 92197878 9.770000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G228000 chr1B 409616585 409624064 7479 True 6763.000000 7245 100.000000 1 7480 2 chr1B.!!$R3 7479
1 TraesCS1B01G228000 chr1B 162187038 162187755 717 False 948.000000 948 90.470000 6737 7459 1 chr1B.!!$F1 722
2 TraesCS1B01G228000 chr1D 302704811 302710876 6065 True 2270.200000 4813 93.401250 765 6734 4 chr1D.!!$R1 5969
3 TraesCS1B01G228000 chr1A 377222820 377229556 6736 True 3341.333333 4211 94.138333 8 6733 3 chr1A.!!$R1 6725
4 TraesCS1B01G228000 chr7B 438373515 438374182 667 False 837.000000 837 89.302000 6801 7470 1 chr7B.!!$F1 669
5 TraesCS1B01G228000 chr4B 214742212 214742950 738 True 785.000000 785 85.906000 6738 7479 1 chr4B.!!$R1 741
6 TraesCS1B01G228000 chr6A 147953874 147954609 735 True 739.000000 739 84.906000 6740 7476 1 chr6A.!!$R2 736
7 TraesCS1B01G228000 chr6A 102993124 102993850 726 True 715.000000 715 84.553000 6740 7470 1 chr6A.!!$R1 730
8 TraesCS1B01G228000 chr5A 383827494 383828226 732 True 732.000000 732 84.812000 6739 7476 1 chr5A.!!$R2 737
9 TraesCS1B01G228000 chr5A 314740921 314741651 730 True 704.000000 704 84.168000 6735 7468 1 chr5A.!!$R1 733
10 TraesCS1B01G228000 chr7A 139443256 139443986 730 True 699.000000 699 84.011000 6740 7472 1 chr7A.!!$R1 732
11 TraesCS1B01G228000 chr7A 701399396 701400132 736 True 691.000000 691 83.780000 6740 7476 1 chr7A.!!$R3 736
12 TraesCS1B01G228000 chr3D 552653725 552658111 4386 True 228.333333 233 86.524333 4859 5342 3 chr3D.!!$R1 483

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
270 271 0.108186 TGAGAGGGCGCACAATACTG 60.108 55.000 14.57 0.0 0.00 2.74 F
1223 1238 2.354403 CGAGTAATTTGGTCGTTCCCCT 60.354 50.000 0.00 0.0 34.77 4.79 F
1474 1499 0.320247 GCACACTGAGCACTAGCAGT 60.320 55.000 0.00 0.0 45.62 4.40 F
1810 1869 0.457851 ATGTGTAGTCTGCCGAGAGC 59.542 55.000 0.00 0.0 44.14 4.09 F
2604 2664 0.318955 ACATGCCTTTTGCGTTGCTC 60.319 50.000 0.00 0.0 45.60 4.26 F
2637 2701 0.394192 TGGTTGAGTCAGCAGAGGTG 59.606 55.000 9.35 0.0 0.00 4.00 F
2942 3006 0.940126 GCAAGGTCGATGGCTATGTG 59.060 55.000 0.00 0.0 0.00 3.21 F
3177 3242 3.054948 CGGTGGGAAGGTAGACCAAATTA 60.055 47.826 0.66 0.0 38.89 1.40 F
4659 4838 2.096220 ATGCTTGCTCACTGTCTCAG 57.904 50.000 0.00 0.0 37.52 3.35 F
5295 7502 0.674895 AGCGTGCTCTTTGGTCATCC 60.675 55.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1321 0.178801 ACTCCCCTCCCCCAAAAGAT 60.179 55.000 0.00 0.00 0.00 2.40 R
2090 2149 0.321671 GCTAGTCCTGGCTTGTCACA 59.678 55.000 0.00 0.00 34.00 3.58 R
2547 2607 0.940126 CAGCATACCTCGCATCCAAC 59.060 55.000 0.00 0.00 0.00 3.77 R
2909 2973 1.070601 ACCTTGCCATTGTTTCCAAGC 59.929 47.619 0.00 0.00 34.76 4.01 R
3854 3921 2.328819 GCAGTCTGCTTCAGGATCAT 57.671 50.000 17.89 0.00 40.96 2.45 R
4476 4655 3.243201 CCTCCAGAAAAGGATATTTGCGC 60.243 47.826 0.00 0.00 36.99 6.09 R
4659 4838 2.821969 ACATGCCACTGAACTTTGATCC 59.178 45.455 0.00 0.00 0.00 3.36 R
4677 4856 4.529377 AGAAACTTGGATGGATGCAAACAT 59.471 37.500 6.23 6.23 37.67 2.71 R
5539 7746 1.318158 CCCACAGCCAGCAATTCCTC 61.318 60.000 0.00 0.00 0.00 3.71 R
6852 9091 0.878416 TTTACACACGCATGCCCTTC 59.122 50.000 13.15 0.00 0.00 3.46 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
49 50 8.668510 AATTTATAGCTCAATCGAACATGAGT 57.331 30.769 20.51 13.15 43.91 3.41
60 61 9.521503 TCAATCGAACATGAGTAAATTAGAGAG 57.478 33.333 0.00 0.00 0.00 3.20
65 66 9.416794 CGAACATGAGTAAATTAGAGAGCATAT 57.583 33.333 0.00 0.00 0.00 1.78
106 107 5.443185 TGACAAAGCTCCTTGAGAAATTG 57.557 39.130 5.15 0.00 0.00 2.32
112 113 4.723309 AGCTCCTTGAGAAATTGTTGACT 58.277 39.130 0.00 0.00 0.00 3.41
153 154 4.380867 CCCAATTCCAAATTGAAGACCTCG 60.381 45.833 12.73 0.00 0.00 4.63
185 186 3.763897 GAGCCCTTGAAAATTAGGAAGCA 59.236 43.478 0.00 0.00 33.13 3.91
187 188 5.518865 AGCCCTTGAAAATTAGGAAGCATA 58.481 37.500 0.00 0.00 33.13 3.14
232 233 9.956720 AAAGAAAAATAGATGTTGTGAAGACTG 57.043 29.630 0.00 0.00 0.00 3.51
233 234 8.908786 AGAAAAATAGATGTTGTGAAGACTGA 57.091 30.769 0.00 0.00 0.00 3.41
240 241 7.840342 AGATGTTGTGAAGACTGATATGTTC 57.160 36.000 0.00 0.00 0.00 3.18
259 260 2.119495 TCCTTTAGATGGTGAGAGGGC 58.881 52.381 0.00 0.00 0.00 5.19
270 271 0.108186 TGAGAGGGCGCACAATACTG 60.108 55.000 14.57 0.00 0.00 2.74
314 315 8.736742 GTTGTTGCTGATTAATTTATGTGATCG 58.263 33.333 0.00 0.00 0.00 3.69
316 317 8.458052 TGTTGCTGATTAATTTATGTGATCGTT 58.542 29.630 0.00 0.00 0.00 3.85
318 319 7.416817 TGCTGATTAATTTATGTGATCGTTGG 58.583 34.615 0.00 0.00 0.00 3.77
319 320 6.360681 GCTGATTAATTTATGTGATCGTTGGC 59.639 38.462 0.00 0.00 0.00 4.52
343 344 7.144000 GCCTAGTCAAAATCATGATCAAATCC 58.856 38.462 9.06 0.00 0.00 3.01
344 345 7.201848 GCCTAGTCAAAATCATGATCAAATCCA 60.202 37.037 9.06 0.00 0.00 3.41
363 364 8.981647 CAAATCCAAAACTAAATTCCTCAACTG 58.018 33.333 0.00 0.00 0.00 3.16
369 370 9.748708 CAAAACTAAATTCCTCAACTGAATGAA 57.251 29.630 0.00 0.00 32.91 2.57
389 390 8.779354 AATGAAAGAGCTCGTTAAGAAATAGT 57.221 30.769 15.11 0.00 0.00 2.12
452 453 4.424842 TCTCAATTTAAATGGGTGGGCTT 58.575 39.130 0.39 0.00 0.00 4.35
465 466 3.195610 GGGTGGGCTTCAAAATTAGGAAG 59.804 47.826 12.40 12.40 42.62 3.46
485 486 6.837568 AGGAAGCATGGTGAATTAGATGATTT 59.162 34.615 0.00 0.00 0.00 2.17
486 487 8.000709 AGGAAGCATGGTGAATTAGATGATTTA 58.999 33.333 0.00 0.00 0.00 1.40
487 488 8.295288 GGAAGCATGGTGAATTAGATGATTTAG 58.705 37.037 0.00 0.00 0.00 1.85
488 489 7.756395 AGCATGGTGAATTAGATGATTTAGG 57.244 36.000 0.00 0.00 0.00 2.69
489 490 7.520798 AGCATGGTGAATTAGATGATTTAGGA 58.479 34.615 0.00 0.00 0.00 2.94
524 525 8.746530 AGATGCTATGAGAAATCATGTGTTTTT 58.253 29.630 1.04 0.00 0.00 1.94
561 562 5.066505 GGGACTGATATGTTTTTACAGGCTG 59.933 44.000 14.16 14.16 36.89 4.85
578 579 3.149981 GGCTGGTTCCTGCCTATTAATC 58.850 50.000 25.50 3.81 44.32 1.75
579 580 3.435026 GGCTGGTTCCTGCCTATTAATCA 60.435 47.826 25.50 0.00 44.32 2.57
586 587 7.665559 TGGTTCCTGCCTATTAATCATTGATAC 59.334 37.037 0.00 0.00 0.00 2.24
641 642 7.309770 AGTACCTCAAATGAAAGAGAGAAGT 57.690 36.000 0.00 0.00 33.74 3.01
643 644 5.233988 ACCTCAAATGAAAGAGAGAAGTCG 58.766 41.667 0.00 0.00 33.74 4.18
646 647 6.347240 CCTCAAATGAAAGAGAGAAGTCGTTG 60.347 42.308 0.00 0.00 33.74 4.10
660 661 6.513180 AGAAGTCGTTGAGAAATAGTTGACA 58.487 36.000 0.00 0.00 0.00 3.58
715 716 8.843308 AAAAATCTCAATTGAATGGATAGGGA 57.157 30.769 9.88 0.23 0.00 4.20
718 719 4.352001 TCTCAATTGAATGGATAGGGAGGG 59.648 45.833 9.88 0.00 0.00 4.30
735 737 3.057245 GGAGGGTCAAAATCAAGAAGCAC 60.057 47.826 0.00 0.00 0.00 4.40
737 739 3.960102 AGGGTCAAAATCAAGAAGCACAA 59.040 39.130 0.00 0.00 0.00 3.33
779 781 4.514401 ACATCTCAATCCTACGTTTTCCC 58.486 43.478 0.00 0.00 0.00 3.97
783 785 5.627135 TCTCAATCCTACGTTTTCCCTTTT 58.373 37.500 0.00 0.00 0.00 2.27
876 880 3.181497 CCAGTTTTCATATCCAACGGCTG 60.181 47.826 0.00 0.00 0.00 4.85
1215 1230 6.493116 TCGACTAGATTCGAGTAATTTGGTC 58.507 40.000 0.00 0.00 43.01 4.02
1223 1238 2.354403 CGAGTAATTTGGTCGTTCCCCT 60.354 50.000 0.00 0.00 34.77 4.79
1244 1259 4.120589 CTGTTTTAGGAGATCGTTAGGCC 58.879 47.826 0.00 0.00 0.00 5.19
1337 1355 1.079057 GGGAGTTTCTCGGTCTGCC 60.079 63.158 0.00 0.00 33.07 4.85
1471 1496 1.004560 TGGCACACTGAGCACTAGC 60.005 57.895 0.69 0.00 42.56 3.42
1472 1497 1.004560 GGCACACTGAGCACTAGCA 60.005 57.895 0.69 0.00 45.49 3.49
1473 1498 1.018226 GGCACACTGAGCACTAGCAG 61.018 60.000 0.69 0.00 45.49 4.24
1474 1499 0.320247 GCACACTGAGCACTAGCAGT 60.320 55.000 0.00 0.00 45.62 4.40
1475 1500 1.067565 GCACACTGAGCACTAGCAGTA 60.068 52.381 0.00 0.00 43.06 2.74
1496 1522 6.543465 CAGTATGGCAAAATCTTGATAGGACA 59.457 38.462 0.00 0.00 34.14 4.02
1497 1523 6.769822 AGTATGGCAAAATCTTGATAGGACAG 59.230 38.462 0.00 0.00 34.14 3.51
1519 1545 6.000219 CAGTTAAGAATGGGTGCTGCTATAT 59.000 40.000 0.00 0.00 0.00 0.86
1520 1546 7.161404 CAGTTAAGAATGGGTGCTGCTATATA 58.839 38.462 0.00 0.00 0.00 0.86
1603 1629 0.535102 AAACAACCCTGAGCACCTCG 60.535 55.000 0.00 0.00 32.35 4.63
1668 1694 3.121030 CCTTGCCAACGGAGCGAG 61.121 66.667 4.35 4.35 40.81 5.03
1712 1771 1.886886 TTTTAGCGCGGGAAAGTTCT 58.113 45.000 8.83 0.00 0.00 3.01
1752 1811 6.868339 GGATGGGTGTAAGAAGAATGTTTTTG 59.132 38.462 0.00 0.00 0.00 2.44
1753 1812 6.783708 TGGGTGTAAGAAGAATGTTTTTGT 57.216 33.333 0.00 0.00 0.00 2.83
1756 1815 8.097662 TGGGTGTAAGAAGAATGTTTTTGTTTT 58.902 29.630 0.00 0.00 0.00 2.43
1803 1862 3.059352 AGGTTTCCATGTGTAGTCTGC 57.941 47.619 0.00 0.00 0.00 4.26
1804 1863 2.084546 GGTTTCCATGTGTAGTCTGCC 58.915 52.381 0.00 0.00 0.00 4.85
1805 1864 1.732259 GTTTCCATGTGTAGTCTGCCG 59.268 52.381 0.00 0.00 0.00 5.69
1806 1865 1.262417 TTCCATGTGTAGTCTGCCGA 58.738 50.000 0.00 0.00 0.00 5.54
1807 1866 0.817654 TCCATGTGTAGTCTGCCGAG 59.182 55.000 0.00 0.00 0.00 4.63
1808 1867 0.817654 CCATGTGTAGTCTGCCGAGA 59.182 55.000 0.00 0.00 0.00 4.04
1809 1868 1.202348 CCATGTGTAGTCTGCCGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
1810 1869 0.457851 ATGTGTAGTCTGCCGAGAGC 59.542 55.000 0.00 0.00 44.14 4.09
1813 1872 2.829003 TAGTCTGCCGAGAGCCCG 60.829 66.667 0.00 0.00 42.71 6.13
1906 1965 2.354805 GGGAGTTTATCGGTCTGCTGTT 60.355 50.000 0.00 0.00 0.00 3.16
2063 2122 4.322650 GCAAAATCTTCACTGGGCCATTAA 60.323 41.667 6.72 0.44 0.00 1.40
2064 2123 5.792741 CAAAATCTTCACTGGGCCATTAAA 58.207 37.500 6.72 0.07 0.00 1.52
2092 2151 8.934023 TGGGTTCTACATCTCTTTTTAATTGT 57.066 30.769 0.00 0.00 0.00 2.71
2236 2295 1.676057 GACACTCTGTTCTCGTCACG 58.324 55.000 0.00 0.00 0.00 4.35
2265 2325 6.588719 TTTTGGATGGGTGTAAGAAGAATG 57.411 37.500 0.00 0.00 0.00 2.67
2495 2555 5.471424 TCTAATTCCTCTCCATGGACTGAT 58.529 41.667 11.44 0.00 32.65 2.90
2547 2607 2.534298 CTCTTGAGCACTGGATACACG 58.466 52.381 0.00 0.00 46.17 4.49
2597 2657 3.641437 TGTCTGTAACATGCCTTTTGC 57.359 42.857 0.00 0.00 34.67 3.68
2604 2664 0.318955 ACATGCCTTTTGCGTTGCTC 60.319 50.000 0.00 0.00 45.60 4.26
2634 2698 2.289882 TGGATTGGTTGAGTCAGCAGAG 60.290 50.000 9.35 0.00 0.00 3.35
2637 2701 0.394192 TGGTTGAGTCAGCAGAGGTG 59.606 55.000 9.35 0.00 0.00 4.00
2676 2740 4.601857 TCCACACTTCCTATTTTTCTCCCT 59.398 41.667 0.00 0.00 0.00 4.20
2942 3006 0.940126 GCAAGGTCGATGGCTATGTG 59.060 55.000 0.00 0.00 0.00 3.21
2949 3013 4.587262 AGGTCGATGGCTATGTGTACAATA 59.413 41.667 0.00 0.00 0.00 1.90
2967 3031 9.088987 TGTACAATATCCAAGTGCTATCTATGA 57.911 33.333 0.00 0.00 0.00 2.15
2987 3051 3.643320 TGATAGGAACCATACAGGAGCAG 59.357 47.826 0.00 0.00 41.22 4.24
3107 3172 7.388224 CCGTCTAAGCTATCTATTGACTACTCA 59.612 40.741 0.00 0.00 0.00 3.41
3177 3242 3.054948 CGGTGGGAAGGTAGACCAAATTA 60.055 47.826 0.66 0.00 38.89 1.40
3187 3252 5.964477 AGGTAGACCAAATTATGTCTCCTGA 59.036 40.000 11.80 0.00 40.84 3.86
3322 3387 3.944015 AGTGAGTTGCAGAAGATAATGCC 59.056 43.478 0.00 0.00 41.85 4.40
3548 3615 4.082245 AGTGTGCTACTTGTTTGTTTGCTT 60.082 37.500 0.00 0.00 35.67 3.91
3774 3841 7.345691 TCTCCATATGCTGAATTCCTACAAAA 58.654 34.615 2.27 0.00 0.00 2.44
3786 3853 9.558396 TGAATTCCTACAAAAATTGATTGCTTT 57.442 25.926 2.27 0.00 0.00 3.51
3837 3904 3.520691 AGTGGTATGAGGCCGTATCTA 57.479 47.619 0.00 0.00 0.00 1.98
3841 3908 6.195700 AGTGGTATGAGGCCGTATCTATAAT 58.804 40.000 0.00 0.00 0.00 1.28
3844 3911 7.067859 GTGGTATGAGGCCGTATCTATAATACA 59.932 40.741 0.00 0.00 0.00 2.29
3854 3921 7.489160 CCGTATCTATAATACAGCAGCCATTA 58.511 38.462 0.00 0.00 0.00 1.90
3900 3967 5.163764 CGCAATGCTCCATCTTAGTTAAACA 60.164 40.000 2.94 0.00 0.00 2.83
3904 3971 8.946085 CAATGCTCCATCTTAGTTAAACACTTA 58.054 33.333 0.00 0.00 36.88 2.24
3905 3972 7.900782 TGCTCCATCTTAGTTAAACACTTAC 57.099 36.000 0.00 0.00 36.88 2.34
3920 3991 6.449635 AACACTTACAGCATCTTGTTTTGA 57.550 33.333 0.00 0.00 32.56 2.69
4123 4267 7.594351 TTATGCCATGTGCCTTGAATATTTA 57.406 32.000 4.07 0.00 40.16 1.40
4226 4404 7.115414 AGGCTGAAATGTCTATAGAAGCTTTT 58.885 34.615 17.24 10.99 0.00 2.27
4391 4570 6.600882 ATGATTTTGCTTGGTTGATCTTCT 57.399 33.333 0.00 0.00 0.00 2.85
4399 4578 5.713389 TGCTTGGTTGATCTTCTTTCATGAT 59.287 36.000 0.00 0.00 0.00 2.45
4476 4655 6.086765 GCATTTATTTCTCAACACTTCACACG 59.913 38.462 0.00 0.00 0.00 4.49
4659 4838 2.096220 ATGCTTGCTCACTGTCTCAG 57.904 50.000 0.00 0.00 37.52 3.35
4677 4856 2.106338 TCAGGATCAAAGTTCAGTGGCA 59.894 45.455 0.00 0.00 0.00 4.92
4786 4965 6.998074 AGATTGTGGTACTTCTGAAATTGTGA 59.002 34.615 0.00 0.00 0.00 3.58
5295 7502 0.674895 AGCGTGCTCTTTGGTCATCC 60.675 55.000 0.00 0.00 0.00 3.51
5319 7526 5.620654 CGCAGTTCCTGAAATCATGTCAAAT 60.621 40.000 0.00 0.00 32.44 2.32
5374 7581 3.037851 TGTCAGAGCAGGTAGATCCAT 57.962 47.619 0.00 0.00 39.02 3.41
5395 7602 6.897966 TCCATTTACTTCTGTATGAGGTCTCT 59.102 38.462 0.00 0.00 36.38 3.10
5396 7603 7.400339 TCCATTTACTTCTGTATGAGGTCTCTT 59.600 37.037 0.00 0.00 36.38 2.85
5515 7722 7.223971 TGTTTGATTCCATAGCACGTACTATTC 59.776 37.037 5.53 2.45 30.26 1.75
5560 7767 1.304381 GAATTGCTGGCTGTGGGGA 60.304 57.895 0.00 0.00 0.00 4.81
5668 7875 2.519302 GGGTTGCACTGCACCTGT 60.519 61.111 17.10 0.00 38.71 4.00
5702 7909 5.189180 GGATTGATTACAACAGAGGAAGCT 58.811 41.667 0.00 0.00 38.90 3.74
5891 8098 0.461961 GCGCTCCTATCAGTGACCTT 59.538 55.000 0.00 0.00 0.00 3.50
5928 8153 0.759346 ATCCCATACTCAGGTTCGGC 59.241 55.000 0.00 0.00 0.00 5.54
5929 8154 0.325296 TCCCATACTCAGGTTCGGCT 60.325 55.000 0.00 0.00 0.00 5.52
5930 8155 0.541863 CCCATACTCAGGTTCGGCTT 59.458 55.000 0.00 0.00 0.00 4.35
5931 8156 1.065418 CCCATACTCAGGTTCGGCTTT 60.065 52.381 0.00 0.00 0.00 3.51
5932 8157 2.009774 CCATACTCAGGTTCGGCTTTG 58.990 52.381 0.00 0.00 0.00 2.77
5933 8158 2.615493 CCATACTCAGGTTCGGCTTTGT 60.615 50.000 0.00 0.00 0.00 2.83
5934 8159 2.922740 TACTCAGGTTCGGCTTTGTT 57.077 45.000 0.00 0.00 0.00 2.83
5935 8160 2.052782 ACTCAGGTTCGGCTTTGTTT 57.947 45.000 0.00 0.00 0.00 2.83
5936 8161 1.947456 ACTCAGGTTCGGCTTTGTTTC 59.053 47.619 0.00 0.00 0.00 2.78
5937 8162 0.941542 TCAGGTTCGGCTTTGTTTCG 59.058 50.000 0.00 0.00 0.00 3.46
5938 8163 0.941542 CAGGTTCGGCTTTGTTTCGA 59.058 50.000 0.00 0.00 0.00 3.71
5939 8164 1.535462 CAGGTTCGGCTTTGTTTCGAT 59.465 47.619 0.00 0.00 32.80 3.59
5940 8165 2.031157 CAGGTTCGGCTTTGTTTCGATT 60.031 45.455 0.00 0.00 32.80 3.34
5941 8166 2.225727 AGGTTCGGCTTTGTTTCGATTC 59.774 45.455 0.00 0.00 32.80 2.52
5942 8167 2.230864 GTTCGGCTTTGTTTCGATTCG 58.769 47.619 0.00 0.00 32.80 3.34
5943 8168 1.785768 TCGGCTTTGTTTCGATTCGA 58.214 45.000 4.29 4.29 0.00 3.71
5944 8169 2.343101 TCGGCTTTGTTTCGATTCGAT 58.657 42.857 9.96 0.00 35.23 3.59
5945 8170 2.093625 TCGGCTTTGTTTCGATTCGATG 59.906 45.455 9.96 0.00 35.23 3.84
6076 8301 2.880890 AGCACACTGAACTTCCATTCAC 59.119 45.455 0.00 0.00 34.84 3.18
6077 8302 2.880890 GCACACTGAACTTCCATTCACT 59.119 45.455 0.00 0.00 34.84 3.41
6255 8485 3.159472 TGAAGAGTTCATGGCATGCTTT 58.841 40.909 22.56 9.63 34.08 3.51
6352 8583 7.596995 AGCGATTACTTAGCAGAAATAGATGAC 59.403 37.037 0.00 0.00 0.00 3.06
6376 8607 6.439375 ACCCTAGTGTACAATTAGACATGACA 59.561 38.462 0.00 0.00 0.00 3.58
6460 8691 5.752955 TGCAGATTTTCCTTTTTGCAAGTAC 59.247 36.000 0.00 0.00 38.47 2.73
6508 8742 3.572682 AGTTTCCCCATTTCGAAGTTTCC 59.427 43.478 0.00 0.00 0.00 3.13
6509 8743 2.209690 TCCCCATTTCGAAGTTTCCC 57.790 50.000 0.00 0.00 0.00 3.97
6534 8768 7.495606 CCATTGATAAAAGTAGAAAAATGCCCC 59.504 37.037 0.00 0.00 0.00 5.80
6540 8776 0.321741 TAGAAAAATGCCCCGTGCGA 60.322 50.000 0.00 0.00 45.60 5.10
6568 8804 6.469275 GCGGAAATGTTCTAAATTAAGCTGTC 59.531 38.462 0.00 0.00 0.00 3.51
6665 8904 2.026822 CAGATGCCAAGAGTACACCCTT 60.027 50.000 0.00 0.00 0.00 3.95
6714 8953 3.118629 TCCATGACAACTATGCTGGACTC 60.119 47.826 0.00 0.00 0.00 3.36
6751 8990 1.078426 CCCCCTTGTCACGCCTAAG 60.078 63.158 0.00 0.00 0.00 2.18
6755 8994 0.037326 CCTTGTCACGCCTAAGCAGA 60.037 55.000 0.00 0.00 39.83 4.26
6854 9093 4.738998 CCGCATGTGGCCAGGGAA 62.739 66.667 13.39 0.00 40.31 3.97
6876 9115 1.269309 GGCATGCGTGTGTAAACCAAA 60.269 47.619 12.44 0.00 0.00 3.28
6900 9140 5.308237 ACTCTGTATCCAAACTTTCCTCTGT 59.692 40.000 0.00 0.00 0.00 3.41
6912 9153 2.856760 TCCTCTGTAATCTCAGCCCT 57.143 50.000 0.00 0.00 35.63 5.19
6913 9154 3.121929 TCCTCTGTAATCTCAGCCCTT 57.878 47.619 0.00 0.00 35.63 3.95
6918 9159 5.495640 CTCTGTAATCTCAGCCCTTTTCTT 58.504 41.667 0.00 0.00 35.63 2.52
6933 9176 3.356529 TTTCTTCAAGCTCATCCCCTC 57.643 47.619 0.00 0.00 0.00 4.30
6934 9177 2.260639 TCTTCAAGCTCATCCCCTCT 57.739 50.000 0.00 0.00 0.00 3.69
6938 9181 0.388659 CAAGCTCATCCCCTCTCTCG 59.611 60.000 0.00 0.00 0.00 4.04
6957 9201 2.234296 CCTGCTCCCTCAACCCCTT 61.234 63.158 0.00 0.00 0.00 3.95
6966 9210 3.115390 CCCTCAACCCCTTTCTAGATCA 58.885 50.000 0.00 0.00 0.00 2.92
6967 9211 3.718956 CCCTCAACCCCTTTCTAGATCAT 59.281 47.826 0.00 0.00 0.00 2.45
6974 9218 4.093011 CCCCTTTCTAGATCATCGATCCT 58.907 47.826 0.00 0.00 39.66 3.24
7006 9251 4.193090 TCGCGGACATTACATTGGTATTT 58.807 39.130 6.13 0.00 0.00 1.40
7042 9292 3.136123 CCCCTCACCATTGCTGCG 61.136 66.667 0.00 0.00 0.00 5.18
7061 9889 2.434359 CGTCGGAGTTTGGGAGGC 60.434 66.667 0.00 0.00 0.00 4.70
7179 10029 4.148825 CCCTCGAAGCCCTCCGTG 62.149 72.222 0.00 0.00 0.00 4.94
7258 10108 0.900647 CGACTCCCTCCTCACCAAGT 60.901 60.000 0.00 0.00 0.00 3.16
7317 10167 1.537202 GCGCAACTCTCCTTCAACAAT 59.463 47.619 0.30 0.00 0.00 2.71
7405 10255 3.112709 GCAAGACCGTCGACTGCC 61.113 66.667 14.70 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.668510 ACTCATGTTCGATTGAGCTATAAATT 57.331 30.769 16.22 0.00 42.51 1.82
25 26 9.764363 TTACTCATGTTCGATTGAGCTATAAAT 57.236 29.630 16.22 0.00 42.51 1.40
26 27 9.594478 TTTACTCATGTTCGATTGAGCTATAAA 57.406 29.630 16.22 12.08 42.51 1.40
27 28 9.764363 ATTTACTCATGTTCGATTGAGCTATAA 57.236 29.630 16.22 8.30 42.51 0.98
35 36 8.272176 GCTCTCTAATTTACTCATGTTCGATTG 58.728 37.037 0.00 0.00 0.00 2.67
81 82 5.695851 TTTCTCAAGGAGCTTTGTCATTC 57.304 39.130 0.00 0.00 0.00 2.67
106 107 7.084486 GGTCATCCAATTTTAACTGAGTCAAC 58.916 38.462 0.00 0.00 0.00 3.18
137 138 5.824904 ATCAATCGAGGTCTTCAATTTGG 57.175 39.130 0.00 0.00 0.00 3.28
153 154 9.688592 CTAATTTTCAAGGGCTCATAATCAATC 57.311 33.333 0.00 0.00 0.00 2.67
206 207 9.956720 CAGTCTTCACAACATCTATTTTTCTTT 57.043 29.630 0.00 0.00 0.00 2.52
207 208 9.342308 TCAGTCTTCACAACATCTATTTTTCTT 57.658 29.630 0.00 0.00 0.00 2.52
223 224 9.039870 CATCTAAAGGAACATATCAGTCTTCAC 57.960 37.037 0.00 0.00 0.00 3.18
224 225 8.206867 CCATCTAAAGGAACATATCAGTCTTCA 58.793 37.037 0.00 0.00 0.00 3.02
232 233 7.158021 CCTCTCACCATCTAAAGGAACATATC 58.842 42.308 0.00 0.00 0.00 1.63
233 234 6.043706 CCCTCTCACCATCTAAAGGAACATAT 59.956 42.308 0.00 0.00 0.00 1.78
240 241 1.202580 CGCCCTCTCACCATCTAAAGG 60.203 57.143 0.00 0.00 0.00 3.11
259 260 5.684850 TGTAAAACACATCAGTATTGTGCG 58.315 37.500 3.85 0.00 46.65 5.34
270 271 8.504005 AGCAACAACTACTATGTAAAACACATC 58.496 33.333 0.00 0.00 44.99 3.06
287 288 9.793252 GATCACATAAATTAATCAGCAACAACT 57.207 29.630 0.00 0.00 0.00 3.16
309 310 3.410631 TTTTGACTAGGCCAACGATCA 57.589 42.857 5.01 0.00 0.00 2.92
314 315 5.357878 TGATCATGATTTTGACTAGGCCAAC 59.642 40.000 10.14 0.00 0.00 3.77
316 317 5.114764 TGATCATGATTTTGACTAGGCCA 57.885 39.130 10.14 0.00 0.00 5.36
318 319 7.144000 GGATTTGATCATGATTTTGACTAGGC 58.856 38.462 10.14 0.00 0.00 3.93
319 320 8.229253 TGGATTTGATCATGATTTTGACTAGG 57.771 34.615 10.14 0.00 0.00 3.02
343 344 9.748708 TTCATTCAGTTGAGGAATTTAGTTTTG 57.251 29.630 0.00 0.00 32.86 2.44
350 351 6.492772 AGCTCTTTCATTCAGTTGAGGAATTT 59.507 34.615 0.00 0.00 32.86 1.82
354 355 4.573900 GAGCTCTTTCATTCAGTTGAGGA 58.426 43.478 6.43 0.00 0.00 3.71
355 356 3.370366 CGAGCTCTTTCATTCAGTTGAGG 59.630 47.826 12.85 0.00 0.00 3.86
363 364 8.874816 ACTATTTCTTAACGAGCTCTTTCATTC 58.125 33.333 12.85 0.00 0.00 2.67
369 370 8.254508 AGATCAACTATTTCTTAACGAGCTCTT 58.745 33.333 12.85 7.82 0.00 2.85
425 426 6.710278 CCCACCCATTTAAATTGAGATGTTT 58.290 36.000 0.00 0.00 0.00 2.83
430 431 4.059773 AGCCCACCCATTTAAATTGAGA 57.940 40.909 0.00 0.00 0.00 3.27
435 436 5.574970 TTTTGAAGCCCACCCATTTAAAT 57.425 34.783 0.00 0.00 0.00 1.40
452 453 6.855763 ATTCACCATGCTTCCTAATTTTGA 57.144 33.333 0.00 0.00 0.00 2.69
465 466 7.750229 TCCTAAATCATCTAATTCACCATGC 57.250 36.000 0.00 0.00 0.00 4.06
524 525 1.566703 TCAGTCCCCTGAACCAACAAA 59.433 47.619 0.00 0.00 44.67 2.83
526 527 2.938301 TCAGTCCCCTGAACCAACA 58.062 52.632 0.00 0.00 44.67 3.33
536 537 4.338400 GCCTGTAAAAACATATCAGTCCCC 59.662 45.833 0.00 0.00 0.00 4.81
539 540 5.648092 ACCAGCCTGTAAAAACATATCAGTC 59.352 40.000 0.00 0.00 0.00 3.51
561 562 7.665559 TGTATCAATGATTAATAGGCAGGAACC 59.334 37.037 0.00 0.00 0.00 3.62
619 620 6.015350 ACGACTTCTCTCTTTCATTTGAGGTA 60.015 38.462 0.00 0.00 0.00 3.08
641 642 4.862350 TCGTGTCAACTATTTCTCAACGA 58.138 39.130 0.00 0.00 0.00 3.85
643 644 9.872757 TTTTTATCGTGTCAACTATTTCTCAAC 57.127 29.630 0.00 0.00 0.00 3.18
660 661 9.703892 TTGAATTTGGTTCATGATTTTTATCGT 57.296 25.926 0.00 0.00 45.77 3.73
701 702 3.144068 TGACCCTCCCTATCCATTCAA 57.856 47.619 0.00 0.00 0.00 2.69
711 712 3.815757 GCTTCTTGATTTTGACCCTCCCT 60.816 47.826 0.00 0.00 0.00 4.20
714 715 3.569701 TGTGCTTCTTGATTTTGACCCTC 59.430 43.478 0.00 0.00 0.00 4.30
715 716 3.565307 TGTGCTTCTTGATTTTGACCCT 58.435 40.909 0.00 0.00 0.00 4.34
718 719 7.647907 ATTCATTGTGCTTCTTGATTTTGAC 57.352 32.000 0.00 0.00 0.00 3.18
783 785 8.877864 TTCATCTCCAAGGCTCTAAATAAAAA 57.122 30.769 0.00 0.00 0.00 1.94
786 788 8.877864 TTTTTCATCTCCAAGGCTCTAAATAA 57.122 30.769 0.00 0.00 0.00 1.40
824 827 3.197790 CCGTCAGATGCCAAGCGG 61.198 66.667 0.00 0.00 0.00 5.52
843 847 0.961753 GAAAACTGGGGTTGCTCCTG 59.038 55.000 0.00 0.00 35.63 3.86
855 859 3.731867 GCAGCCGTTGGATATGAAAACTG 60.732 47.826 0.00 0.00 0.00 3.16
876 880 2.028567 GGAGTGGGATACTGCTATCTGC 60.029 54.545 0.00 0.00 43.69 4.26
957 965 2.962569 GCGGAGGCAAGGGTTTTC 59.037 61.111 0.00 0.00 39.62 2.29
1207 1222 2.375014 AACAGGGGAACGACCAAATT 57.625 45.000 0.00 0.00 41.20 1.82
1223 1238 3.773119 AGGCCTAACGATCTCCTAAAACA 59.227 43.478 1.29 0.00 0.00 2.83
1305 1321 0.178801 ACTCCCCTCCCCCAAAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
1467 1492 6.630444 ATCAAGATTTTGCCATACTGCTAG 57.370 37.500 0.00 0.00 34.21 3.42
1470 1495 5.532406 TCCTATCAAGATTTTGCCATACTGC 59.468 40.000 0.00 0.00 34.21 4.40
1471 1496 6.543465 TGTCCTATCAAGATTTTGCCATACTG 59.457 38.462 0.00 0.00 34.21 2.74
1472 1497 6.662755 TGTCCTATCAAGATTTTGCCATACT 58.337 36.000 0.00 0.00 34.21 2.12
1473 1498 6.543831 ACTGTCCTATCAAGATTTTGCCATAC 59.456 38.462 0.00 0.00 34.21 2.39
1474 1499 6.662755 ACTGTCCTATCAAGATTTTGCCATA 58.337 36.000 0.00 0.00 34.21 2.74
1475 1500 5.513233 ACTGTCCTATCAAGATTTTGCCAT 58.487 37.500 0.00 0.00 34.21 4.40
1496 1522 2.887151 AGCAGCACCCATTCTTAACT 57.113 45.000 0.00 0.00 0.00 2.24
1497 1523 6.934645 TGTATATAGCAGCACCCATTCTTAAC 59.065 38.462 0.00 0.00 0.00 2.01
1520 1546 7.918562 GCTAGTCTCTCGATTAAAAAGAGATGT 59.081 37.037 14.33 9.69 45.26 3.06
1668 1694 4.407296 AGAGATGGTGATAAGAACAGGGTC 59.593 45.833 0.00 0.00 0.00 4.46
1707 1766 9.853177 CCCATCCTAAATAAATCACTAAGAACT 57.147 33.333 0.00 0.00 0.00 3.01
1708 1767 9.628500 ACCCATCCTAAATAAATCACTAAGAAC 57.372 33.333 0.00 0.00 0.00 3.01
1752 1811 4.759516 TTTCAGGTCTAATCGCCAAAAC 57.240 40.909 0.00 0.00 0.00 2.43
1753 1812 4.380444 GCATTTCAGGTCTAATCGCCAAAA 60.380 41.667 0.00 0.00 0.00 2.44
1756 1815 2.288666 GCATTTCAGGTCTAATCGCCA 58.711 47.619 0.00 0.00 0.00 5.69
1803 1862 1.030488 TACAAGTCTCGGGCTCTCGG 61.030 60.000 0.00 0.00 0.00 4.63
1804 1863 1.025812 ATACAAGTCTCGGGCTCTCG 58.974 55.000 0.00 0.00 0.00 4.04
1805 1864 2.427453 TCAATACAAGTCTCGGGCTCTC 59.573 50.000 0.00 0.00 0.00 3.20
1806 1865 2.457598 TCAATACAAGTCTCGGGCTCT 58.542 47.619 0.00 0.00 0.00 4.09
1807 1866 2.930682 GTTCAATACAAGTCTCGGGCTC 59.069 50.000 0.00 0.00 0.00 4.70
1808 1867 2.567615 AGTTCAATACAAGTCTCGGGCT 59.432 45.455 0.00 0.00 0.00 5.19
1809 1868 2.673368 CAGTTCAATACAAGTCTCGGGC 59.327 50.000 0.00 0.00 0.00 6.13
1810 1869 4.188247 TCAGTTCAATACAAGTCTCGGG 57.812 45.455 0.00 0.00 0.00 5.14
1906 1965 1.072391 CACAACCATAAGCACGCGTA 58.928 50.000 13.44 0.00 0.00 4.42
2052 2111 3.519107 AGAACCCATTTTTAATGGCCCAG 59.481 43.478 12.01 2.79 37.85 4.45
2090 2149 0.321671 GCTAGTCCTGGCTTGTCACA 59.678 55.000 0.00 0.00 34.00 3.58
2092 2151 1.553690 GGGCTAGTCCTGGCTTGTCA 61.554 60.000 5.99 0.00 37.24 3.58
2160 2219 2.178521 CCACGTTCGAGTCTCGGG 59.821 66.667 21.63 10.86 40.88 5.14
2286 2346 5.003804 GGAAACCTAGAATTGCAGTTCAGA 58.996 41.667 22.20 9.93 0.00 3.27
2495 2555 7.553760 TCATTTACAGCCGATATATAGGTCGTA 59.446 37.037 12.82 11.07 36.17 3.43
2547 2607 0.940126 CAGCATACCTCGCATCCAAC 59.060 55.000 0.00 0.00 0.00 3.77
2597 2657 4.261322 CCAATCCAAGGATATTGAGCAACG 60.261 45.833 1.29 0.00 35.53 4.10
2604 2664 5.887598 TGACTCAACCAATCCAAGGATATTG 59.112 40.000 1.29 7.91 33.97 1.90
2634 2698 6.201997 GTGTGGAAAAACATTAAATGGACACC 59.798 38.462 0.00 0.00 31.49 4.16
2637 2701 7.170828 GGAAGTGTGGAAAAACATTAAATGGAC 59.829 37.037 0.00 0.00 31.49 4.02
2715 2779 1.826720 GGAAGATTGCCATTTGGAGCA 59.173 47.619 0.00 0.00 37.39 4.26
2781 2845 1.635487 AGTAACCTGACATGGGTGCAT 59.365 47.619 0.00 0.00 37.13 3.96
2909 2973 1.070601 ACCTTGCCATTGTTTCCAAGC 59.929 47.619 0.00 0.00 34.76 4.01
2949 3013 7.093112 GGTTCCTATCATAGATAGCACTTGGAT 60.093 40.741 8.22 0.00 0.00 3.41
2967 3031 3.658725 ACTGCTCCTGTATGGTTCCTAT 58.341 45.455 0.00 0.00 37.07 2.57
2987 3051 1.424493 GCTGCATCACCTCTGCGTAC 61.424 60.000 0.00 0.00 42.62 3.67
3107 3172 1.091771 CCTCAATTCCGTCGCAGCAT 61.092 55.000 0.00 0.00 0.00 3.79
3217 3282 3.740044 TCTTGCTGTGCGTAAAATAGC 57.260 42.857 0.00 0.00 35.06 2.97
3348 3413 9.807921 CAGGGGTTATTTAGGATTATTATGTGT 57.192 33.333 0.00 0.00 0.00 3.72
3358 3425 5.253096 ACAACAGTCAGGGGTTATTTAGGAT 59.747 40.000 0.00 0.00 0.00 3.24
3361 3428 5.768164 ACAACAACAGTCAGGGGTTATTTAG 59.232 40.000 0.00 0.00 0.00 1.85
3362 3429 5.697067 ACAACAACAGTCAGGGGTTATTTA 58.303 37.500 0.00 0.00 0.00 1.40
3365 3432 3.876309 ACAACAACAGTCAGGGGTTAT 57.124 42.857 0.00 0.00 0.00 1.89
3366 3433 4.774660 TTACAACAACAGTCAGGGGTTA 57.225 40.909 0.00 0.00 0.00 2.85
3368 3435 3.486383 CATTACAACAACAGTCAGGGGT 58.514 45.455 0.00 0.00 0.00 4.95
3369 3436 2.819608 CCATTACAACAACAGTCAGGGG 59.180 50.000 0.00 0.00 0.00 4.79
3370 3437 3.486383 ACCATTACAACAACAGTCAGGG 58.514 45.455 0.00 0.00 0.00 4.45
3837 3904 6.827251 CAGGATCATAATGGCTGCTGTATTAT 59.173 38.462 0.00 5.70 0.00 1.28
3841 3908 3.647590 TCAGGATCATAATGGCTGCTGTA 59.352 43.478 0.00 0.00 0.00 2.74
3844 3911 3.752665 CTTCAGGATCATAATGGCTGCT 58.247 45.455 0.00 0.00 0.00 4.24
3854 3921 2.328819 GCAGTCTGCTTCAGGATCAT 57.671 50.000 17.89 0.00 40.96 2.45
3877 3944 6.030228 GTGTTTAACTAAGATGGAGCATTGC 58.970 40.000 0.00 0.00 0.00 3.56
4391 4570 7.648908 GCAACAATCGGATCAAATATCATGAAA 59.351 33.333 0.00 0.00 0.00 2.69
4399 4578 3.947196 AGCTGCAACAATCGGATCAAATA 59.053 39.130 1.02 0.00 0.00 1.40
4476 4655 3.243201 CCTCCAGAAAAGGATATTTGCGC 60.243 47.826 0.00 0.00 36.99 6.09
4659 4838 2.821969 ACATGCCACTGAACTTTGATCC 59.178 45.455 0.00 0.00 0.00 3.36
4677 4856 4.529377 AGAAACTTGGATGGATGCAAACAT 59.471 37.500 6.23 6.23 37.67 2.71
5361 7568 5.675538 ACAGAAGTAAATGGATCTACCTGC 58.324 41.667 0.00 0.00 39.86 4.85
5374 7581 9.085645 TGTTAAGAGACCTCATACAGAAGTAAA 57.914 33.333 0.00 0.00 33.13 2.01
5427 7634 8.849543 AACCCTCCTACTGAGTTAATGTATAA 57.150 34.615 0.00 0.00 39.65 0.98
5503 7710 7.702772 CCAGATCCTATAATGAATAGTACGTGC 59.297 40.741 0.00 0.00 36.57 5.34
5515 7722 9.717942 CTCTTAAAACCTCCAGATCCTATAATG 57.282 37.037 0.00 0.00 0.00 1.90
5539 7746 1.318158 CCCACAGCCAGCAATTCCTC 61.318 60.000 0.00 0.00 0.00 3.71
5560 7767 5.945784 TCAAATTCGTTCCTTCCAAGATCAT 59.054 36.000 0.00 0.00 0.00 2.45
5668 7875 6.157820 TGTTGTAATCAATCCCTCTATCCACA 59.842 38.462 0.00 0.00 35.92 4.17
5891 8098 8.962679 GTATGGGATAAAAAGTATCACCAAACA 58.037 33.333 0.00 0.00 32.27 2.83
5928 8153 4.319115 CAGCAACATCGAATCGAAACAAAG 59.681 41.667 10.12 0.00 39.99 2.77
5929 8154 4.024472 TCAGCAACATCGAATCGAAACAAA 60.024 37.500 10.12 0.00 39.99 2.83
5930 8155 3.496507 TCAGCAACATCGAATCGAAACAA 59.503 39.130 10.12 0.00 39.99 2.83
5931 8156 3.063485 TCAGCAACATCGAATCGAAACA 58.937 40.909 10.12 0.00 39.99 2.83
5932 8157 3.722555 TCAGCAACATCGAATCGAAAC 57.277 42.857 10.12 0.00 39.99 2.78
5933 8158 4.213270 ACTTTCAGCAACATCGAATCGAAA 59.787 37.500 10.12 0.00 39.99 3.46
5934 8159 3.745975 ACTTTCAGCAACATCGAATCGAA 59.254 39.130 10.12 0.00 39.99 3.71
5935 8160 3.123453 CACTTTCAGCAACATCGAATCGA 59.877 43.478 8.12 8.12 41.13 3.59
5936 8161 3.123453 TCACTTTCAGCAACATCGAATCG 59.877 43.478 0.00 0.00 0.00 3.34
5937 8162 4.668576 TCACTTTCAGCAACATCGAATC 57.331 40.909 0.00 0.00 0.00 2.52
5938 8163 5.437289 TTTCACTTTCAGCAACATCGAAT 57.563 34.783 0.00 0.00 0.00 3.34
5939 8164 4.891627 TTTCACTTTCAGCAACATCGAA 57.108 36.364 0.00 0.00 0.00 3.71
5940 8165 4.083324 GGATTTCACTTTCAGCAACATCGA 60.083 41.667 0.00 0.00 0.00 3.59
5941 8166 4.161333 GGATTTCACTTTCAGCAACATCG 58.839 43.478 0.00 0.00 0.00 3.84
5942 8167 5.125100 TGGATTTCACTTTCAGCAACATC 57.875 39.130 0.00 0.00 0.00 3.06
5943 8168 5.733620 ATGGATTTCACTTTCAGCAACAT 57.266 34.783 0.00 0.00 0.00 2.71
5944 8169 5.163426 ACAATGGATTTCACTTTCAGCAACA 60.163 36.000 0.00 0.00 0.00 3.33
5945 8170 5.291971 ACAATGGATTTCACTTTCAGCAAC 58.708 37.500 0.00 0.00 0.00 4.17
6076 8301 9.231297 TCAACTATTTATTCAGAAAGGGTTCAG 57.769 33.333 0.00 0.00 36.09 3.02
6077 8302 9.581289 TTCAACTATTTATTCAGAAAGGGTTCA 57.419 29.630 0.00 0.00 36.09 3.18
6110 8335 2.315925 TGAGTCGGAATGAGAATGGC 57.684 50.000 0.00 0.00 0.00 4.40
6255 8485 2.037687 CCCATGGCTGCCTTTGGA 59.962 61.111 30.54 10.02 32.01 3.53
6352 8583 6.757010 GTGTCATGTCTAATTGTACACTAGGG 59.243 42.308 0.00 0.00 34.41 3.53
6460 8691 3.411446 TGGGATGTGCAAGAAACTACTG 58.589 45.455 0.00 0.00 0.00 2.74
6508 8742 7.495606 GGGGCATTTTTCTACTTTTATCAATGG 59.504 37.037 0.00 0.00 0.00 3.16
6509 8743 7.222611 CGGGGCATTTTTCTACTTTTATCAATG 59.777 37.037 0.00 0.00 0.00 2.82
6534 8768 2.096406 CATTTCCGCTGTCGCACG 59.904 61.111 0.00 0.00 35.30 5.34
6540 8776 6.151144 AGCTTAATTTAGAACATTTCCGCTGT 59.849 34.615 0.00 0.00 0.00 4.40
6568 8804 3.350909 ATGCGCATGTGCCTTGCAG 62.351 57.895 27.42 0.00 40.08 4.41
6706 8945 1.064654 GCAAATCCAATCGAGTCCAGC 59.935 52.381 0.00 0.00 0.00 4.85
6714 8953 3.428862 GGGGTAACTTGCAAATCCAATCG 60.429 47.826 0.00 0.00 0.00 3.34
6751 8990 2.860735 CCTTAGTCACGCTAACATCTGC 59.139 50.000 0.00 0.00 34.95 4.26
6755 8994 2.761208 AGCTCCTTAGTCACGCTAACAT 59.239 45.455 0.00 0.00 34.95 2.71
6850 9089 2.813226 TACACACGCATGCCCTTCCC 62.813 60.000 13.15 0.00 0.00 3.97
6852 9091 0.878416 TTTACACACGCATGCCCTTC 59.122 50.000 13.15 0.00 0.00 3.46
6854 9093 1.241315 GGTTTACACACGCATGCCCT 61.241 55.000 13.15 0.00 0.00 5.19
6900 9140 4.702131 GCTTGAAGAAAAGGGCTGAGATTA 59.298 41.667 0.00 0.00 0.00 1.75
6912 9153 3.331889 AGAGGGGATGAGCTTGAAGAAAA 59.668 43.478 0.00 0.00 0.00 2.29
6913 9154 2.915604 AGAGGGGATGAGCTTGAAGAAA 59.084 45.455 0.00 0.00 0.00 2.52
6918 9159 1.786937 GAGAGAGGGGATGAGCTTGA 58.213 55.000 0.00 0.00 0.00 3.02
6933 9176 2.354401 TTGAGGGAGCAGGCGAGAG 61.354 63.158 0.00 0.00 0.00 3.20
6934 9177 2.283894 TTGAGGGAGCAGGCGAGA 60.284 61.111 0.00 0.00 0.00 4.04
6938 9181 4.432741 GGGGTTGAGGGAGCAGGC 62.433 72.222 0.00 0.00 0.00 4.85
6957 9201 4.287766 TCGGAGGATCGATGATCTAGAA 57.712 45.455 0.54 0.00 38.91 2.10
6987 9232 6.073222 GGCTCTAAATACCAATGTAATGTCCG 60.073 42.308 0.00 0.00 0.00 4.79
6990 9235 8.588290 TTTGGCTCTAAATACCAATGTAATGT 57.412 30.769 0.00 0.00 42.77 2.71
7006 9251 5.402630 AGGGGAAGAAAATTTTTGGCTCTA 58.597 37.500 4.63 0.00 0.00 2.43
7022 9272 1.318158 GCAGCAATGGTGAGGGGAAG 61.318 60.000 17.33 0.00 32.22 3.46
7042 9292 2.434359 CTCCCAAACTCCGACGGC 60.434 66.667 9.66 0.00 0.00 5.68
7052 9303 1.266160 TTACCGATCCGCCTCCCAAA 61.266 55.000 0.00 0.00 0.00 3.28
7061 9889 3.284197 GGTGGATGTTACCGATCCG 57.716 57.895 0.00 0.00 42.22 4.18
7194 10044 0.984961 CTTCCTCCATGGCCTCCAGA 60.985 60.000 6.96 0.00 36.75 3.86
7258 10108 4.415332 GGCGGTCTGCTCGTCGAA 62.415 66.667 3.10 0.00 45.43 3.71
7291 10141 2.217038 AGGAGAGTTGCGCCTCCAA 61.217 57.895 25.92 3.58 44.19 3.53


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

AutoCloner maintained by Alex Coulton.